From 92e3f40640e108271148f6dfcd734ac71636f6db Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20G=C3=B3mez-S=C3=A1nchez?=
 <magicDGS@users.noreply.github.com>
Date: Thu, 30 Aug 2018 15:37:31 +0200
Subject: [PATCH] Release 1.5.2 (#529)

* Release javadoc
* Release documentation site
* Update CHANGELOG
---
 CHANGELOG.md                                  |  4 ++
 docs/_data/index.yml                          |  4 +-
 docs/javadoc/allclasses-frame.html            |  6 +-
 docs/javadoc/allclasses-noframe.html          |  6 +-
 docs/javadoc/constant-values.html             |  8 +--
 docs/javadoc/deprecated-list.html             |  8 +--
 docs/javadoc/help-doc.html                    |  8 +--
 docs/javadoc/index-all.html                   | 20 +++++--
 docs/javadoc/index.html                       |  4 +-
 docs/javadoc/org/magicdgs/readtools/Main.html |  8 +--
 .../org/magicdgs/readtools/RTDefaults.html    |  8 +--
 .../magicdgs/readtools/RTHelpConstants.html   |  8 +--
 .../cmd/RTDeprecatedToolsRegistry.html        |  8 +--
 .../readtools/cmd/RTStandardArguments.html    |  8 +--
 .../BarcodeDetectorArgumentCollection.html    |  8 +--
 ...arcodeWithQualitiesArgumentCollection.html |  8 +--
 ...on.FixSimpleBarcodeArgumentCollection.html |  8 +--
 .../FixBarcodeAbstractArgumentCollection.html |  8 +--
 .../RTInputArgumentCollection.html            |  8 +--
 .../RTOutputArgumentCollection.html           |  8 +--
 .../RTOutputBamArgumentCollection.html        |  8 +--
 .../RTOutputBamSplitArgumentCollection.html   |  8 +--
 .../RTOutputFastqArgumentCollection.html      |  8 +--
 .../ReadGroupArgumentCollection.html          |  8 +--
 .../TrimmerPluginArgumentCollection.html      |  8 +--
 .../argumentcollections/package-frame.html    |  6 +-
 .../argumentcollections/package-summary.html  |  8 +--
 .../cmd/argumentcollections/package-tree.html |  8 +--
 .../magicdgs/readtools/cmd/package-frame.html |  6 +-
 .../readtools/cmd/package-summary.html        |  8 +--
 .../magicdgs/readtools/cmd/package-tree.html  |  8 +--
 .../cmd/plugin/TrimmerPluginDescriptor.html   |  8 +--
 .../readtools/cmd/plugin/package-frame.html   |  6 +-
 .../readtools/cmd/plugin/package-summary.html |  8 +--
 .../readtools/cmd/plugin/package-tree.html    |  8 +--
 .../programgroups/DistmapProgramGroup.html    |  8 +--
 .../MappabiltityProgramGroup.html             |  8 +--
 .../cmd/programgroups/MappedProgramGroup.html |  8 +--
 .../RTConversionProgramGroup.html             |  8 +--
 .../RTManipulationProgramGroup.html           |  8 +--
 .../cmd/programgroups/package-frame.html      |  6 +-
 .../cmd/programgroups/package-summary.html    |  8 +--
 .../cmd/programgroups/package-tree.html       |  8 +--
 .../documentation/RTGSONWorkUnit.html         |  8 +--
 .../RTHelpDocWorkUnitHandler.html             |  8 +--
 .../readtools/documentation/RTHelpDoclet.html |  8 +--
 .../documentation/package-frame.html          |  6 +-
 .../documentation/package-summary.html        |  8 +--
 .../readtools/documentation/package-tree.html |  8 +--
 .../readtools/engine/RTDataSource.html        |  8 +--
 .../readtools/engine/RTReadWalker.html        |  8 +--
 .../readtools/engine/ReadToolsProgram.html    |  8 +--
 .../readtools/engine/ReadToolsWalker.html     |  8 +--
 .../readtools/engine/package-frame.html       |  6 +-
 .../readtools/engine/package-summary.html     |  8 +--
 .../readtools/engine/package-tree.html        |  8 +--
 .../sourcehandler/FastqSourceHandler.html     |  8 +--
 .../sourcehandler/ReadsSourceHandler.html     |  8 +--
 .../sourcehandler/SamSourceHandler.html       |  8 +--
 .../engine/sourcehandler/package-frame.html   |  6 +-
 .../engine/sourcehandler/package-summary.html |  8 +--
 .../engine/sourcehandler/package-tree.html    |  8 +--
 .../RTUserExceptions.InvalidOutputFormat.html |  8 +--
 .../RTUserExceptions.OutputFileExists.html    |  8 +--
 .../exceptions/RTUserExceptions.html          |  8 +--
 .../readtools/exceptions/package-frame.html   |  6 +-
 .../readtools/exceptions/package-summary.html |  8 +--
 .../readtools/exceptions/package-tree.html    |  8 +--
 .../readtools/metrics/FilterMetric.html       |  8 +--
 .../readtools/metrics/TrimmerMetric.html      |  8 +--
 .../metrics/barcodes/BarcodeDetector.html     |  8 +--
 .../metrics/barcodes/BarcodeStat.html         |  8 +--
 .../metrics/barcodes/MatcherStat.html         |  8 +--
 .../metrics/barcodes/package-frame.html       |  6 +-
 .../metrics/barcodes/package-summary.html     |  8 +--
 .../metrics/barcodes/package-tree.html        |  8 +--
 .../readtools/metrics/package-frame.html      |  6 +-
 .../readtools/metrics/package-summary.html    |  8 +--
 .../readtools/metrics/package-tree.html       |  8 +--
 .../org/magicdgs/readtools/package-frame.html |  6 +-
 .../magicdgs/readtools/package-summary.html   |  8 +--
 .../org/magicdgs/readtools/package-tree.html  |  8 +--
 .../barcodes/AssignReadGroupByBarcode.html    |  8 +--
 .../dictionary/BarcodeDictionary.html         |  8 +--
 .../dictionary/BarcodeDictionaryFactory.html  |  8 +--
 .../dictionary/decoder/BarcodeDecoder.html    |  8 +--
 .../dictionary/decoder/BarcodeMatch.html      |  8 +--
 .../dictionary/decoder/package-frame.html     |  6 +-
 .../dictionary/decoder/package-summary.html   |  8 +--
 .../dictionary/decoder/package-tree.html      |  8 +--
 .../barcodes/dictionary/package-frame.html    |  6 +-
 .../barcodes/dictionary/package-summary.html  |  8 +--
 .../barcodes/dictionary/package-tree.html     |  8 +--
 .../tools/barcodes/package-frame.html         |  6 +-
 .../tools/barcodes/package-summary.html       |  8 +--
 .../tools/barcodes/package-tree.html          |  8 +--
 .../tools/conversion/ReadsToFastq.html        |  8 +--
 .../tools/conversion/StandardizeReads.html    |  8 +--
 .../tools/conversion/package-frame.html       |  6 +-
 .../tools/conversion/package-summary.html     |  8 +--
 .../tools/conversion/package-tree.html        |  8 +--
 .../tools/distmap/DownloadDistmapResult.html  |  8 +--
 .../tools/distmap/ReadsToDistmap.html         |  8 +--
 .../tools/distmap/package-frame.html          |  6 +-
 .../tools/distmap/package-summary.html        |  8 +--
 .../readtools/tools/distmap/package-tree.html |  8 +--
 .../mappability/gem/GemMappabilityToBed.html  |  8 +--
 .../tools/mappability/gem/GemScoreMethod.html |  8 +--
 .../tools/mappability/gem/package-frame.html  |  6 +-
 .../mappability/gem/package-summary.html      |  8 +--
 .../tools/mappability/gem/package-tree.html   |  8 +--
 .../mapped/ComputeProperStatByWindow.html     |  8 +--
 .../readtools/tools/mapped/package-frame.html |  6 +-
 .../tools/mapped/package-summary.html         |  8 +--
 .../readtools/tools/mapped/package-tree.html  |  8 +--
 .../quality/QualityEncodingDetector.html      |  8 +--
 .../tools/quality/package-frame.html          |  6 +-
 .../tools/quality/package-summary.html        |  8 +--
 .../readtools/tools/quality/package-tree.html |  8 +--
 .../readtools/tools/trimming/TrimReads.html   |  8 +--
 ...mReadsTrimmerPluginArgumentCollection.html |  8 +--
 .../tools/trimming/package-frame.html         |  6 +-
 .../tools/trimming/package-summary.html       |  8 +--
 .../tools/trimming/package-tree.html          |  8 +--
 .../magicdgs/readtools/utils/HadoopUtils.html |  8 +--
 .../utils/distmap/DistmapEncoder.html         |  8 +--
 .../utils/distmap/DistmapException.html       |  8 +--
 .../utils/distmap/DistmapGATKWriter.html      |  8 +--
 .../utils/distmap/package-frame.html          |  6 +-
 .../utils/distmap/package-summary.html        |  8 +--
 .../readtools/utils/distmap/package-tree.html |  8 +--
 .../readtools/utils/fastq/FastqGATKRead.html  |  8 +--
 .../utils/fastq/FastqGATKWriter.html          |  8 +--
 .../utils/fastq/FastqReadNameEncoding.html    | 12 ++--
 .../utils/fastq/RTFastqConstants.html         |  8 +--
 .../readtools/utils/fastq/package-frame.html  |  6 +-
 .../utils/fastq/package-summary.html          |  8 +--
 .../readtools/utils/fastq/package-tree.html   |  8 +--
 .../utils/function/BinaryPredicate.html       |  8 +--
 .../utils/function/package-frame.html         |  6 +-
 .../utils/function/package-summary.html       |  8 +--
 .../utils/function/package-tree.html          |  8 +--
 .../InterleaveGATKReadIterators.html          |  8 +--
 .../iterators/ReadTransformerIterator.html    |  8 +--
 .../utils/iterators/RecordToReadIterator.html |  8 +--
 .../utils/iterators/package-frame.html        |  6 +-
 .../utils/iterators/package-summary.html      |  8 +--
 .../utils/iterators/package-tree.html         |  8 +--
 .../paired/GATKReadPairedIterator.html        |  8 +--
 .../utils/iterators/paired/package-frame.html |  6 +-
 .../iterators/paired/package-summary.html     |  8 +--
 .../utils/iterators/paired/package-tree.html  |  8 +--
 .../gem/GemMappabilityException.html          |  8 +--
 .../mappability/gem/GemMappabilityHeader.html |  8 +--
 .../mappability/gem/GemMappabilityReader.html |  8 +--
 .../mappability/gem/GemMappabilityRecord.html |  8 +--
 .../utils/mappability/gem/package-frame.html  |  6 +-
 .../mappability/gem/package-summary.html      |  8 +--
 .../utils/mappability/gem/package-tree.html   |  8 +--
 .../utils/math/RelationalOperator.html        |  8 +--
 .../readtools/utils/math/package-frame.html   |  6 +-
 .../readtools/utils/math/package-summary.html |  8 +--
 .../readtools/utils/math/package-tree.html    |  8 +--
 .../readtools/utils/package-frame.html        |  6 +-
 .../readtools/utils/package-summary.html      |  8 +--
 .../readtools/utils/package-tree.html         |  8 +--
 .../readtools/utils/read/RTReadUtils.html     | 58 +++++++++++++++----
 .../utils/read/ReadReaderFactory.html         |  8 +--
 .../utils/read/ReadWriterFactory.html         |  8 +--
 .../readtools/utils/read/ReservedTags.html    |  8 +--
 .../read/filter/CompletelyTrimReadFilter.html |  8 +--
 .../utils/read/filter/package-frame.html      |  6 +-
 .../utils/read/filter/package-summary.html    |  8 +--
 .../utils/read/filter/package-tree.html       |  8 +--
 .../readtools/utils/read/package-frame.html   |  6 +-
 .../readtools/utils/read/package-summary.html |  8 +--
 .../readtools/utils/read/package-tree.html    |  8 +--
 .../read/stats/PairEndReadStatFunction.html   |  8 +--
 .../read/stats/SingleReadStatFunction.html    |  8 +--
 .../utils/read/stats/StatFunction.html        |  8 +--
 .../utils/read/stats/StatFunctionUtils.html   |  8 +--
 .../stats/engine/ProperStatWindowEngine.html  |  8 +--
 .../read/stats/engine/package-frame.html      |  6 +-
 .../read/stats/engine/package-summary.html    |  8 +--
 .../utils/read/stats/engine/package-tree.html |  8 +--
 .../utils/read/stats/package-frame.html       |  6 +-
 .../utils/read/stats/package-summary.html     |  8 +--
 .../utils/read/stats/package-tree.html        |  8 +--
 .../stats/pairstat/PairIntegerTagCounter.html |  8 +--
 .../pairstat/PairIntegerTagListCounter.html   |  8 +--
 .../read/stats/pairstat/package-frame.html    |  6 +-
 .../read/stats/pairstat/package-summary.html  |  8 +--
 .../read/stats/pairstat/package-tree.html     |  8 +--
 .../stats/singlestat/ContainIndelCounter.html |  8 +--
 .../singlestat/ContainSoftclipCounter.html    |  8 +--
 .../read/stats/singlestat/package-frame.html  |  6 +-
 .../stats/singlestat/package-summary.html     |  8 +--
 .../read/stats/singlestat/package-tree.html   |  8 +--
 .../CheckQualityReadTransformer.html          |  8 +--
 .../SolexaToSangerReadTransformer.html        |  8 +--
 .../FixRawBarcodeTagsReadTransformer.html     |  8 +--
 .../FixReadNameBarcodesReadTransformer.html   |  8 +--
 .../transformer/barcodes/package-frame.html   |  6 +-
 .../transformer/barcodes/package-summary.html |  8 +--
 .../transformer/barcodes/package-tree.html    |  8 +--
 .../utils/read/transformer/package-frame.html |  6 +-
 .../read/transformer/package-summary.html     |  8 +--
 .../utils/read/transformer/package-tree.html  |  8 +--
 .../ApplyTrimResultReadTransformer.html       |  8 +--
 .../transformer/trimming/CutReadTrimmer.html  |  8 +--
 .../trimming/MottQualityTrimmer.html          |  8 +--
 .../trimming/TrailingNtrimmer.html            |  8 +--
 .../trimming/TrimmingFunction.html            |  8 +--
 .../transformer/trimming/package-frame.html   |  6 +-
 .../transformer/trimming/package-summary.html |  8 +--
 .../transformer/trimming/package-tree.html    |  8 +--
 .../utils/read/writer/NullGATKWriter.html     |  8 +--
 .../utils/read/writer/PairEndSplitter.html    |  8 +--
 .../writer/ReadToolsIOFormat.BamFormat.html   |  8 +--
 .../writer/ReadToolsIOFormat.FastqFormat.html |  8 +--
 .../utils/read/writer/ReadToolsIOFormat.html  |  8 +--
 .../utils/read/writer/SplitGATKWriter.html    |  8 +--
 .../utils/read/writer/package-frame.html      |  6 +-
 .../utils/read/writer/package-summary.html    |  8 +--
 .../utils/read/writer/package-tree.html       | 10 ++--
 .../utils/trimming/TrimAndFilterPipeline.html |  8 +--
 .../utils/trimming/TrimmingUtil.html          |  8 +--
 .../utils/trimming/package-frame.html         |  6 +-
 .../utils/trimming/package-summary.html       |  8 +--
 .../utils/trimming/package-tree.html          |  8 +--
 docs/javadoc/overview-frame.html              |  6 +-
 docs/javadoc/overview-summary.html            | 10 ++--
 docs/javadoc/overview-tree.html               |  8 +--
 docs/javadoc/serialized-form.html             |  8 +--
 .../AlignmentAgreesWithHeaderReadFilter.md    |  2 +-
 docs/readtools/AllowAllReadsReadFilter.md     |  2 +-
 docs/readtools/AmbiguousBaseReadFilter.md     |  2 +-
 docs/readtools/AssignReadGroupByBarcode.md    |  2 +-
 docs/readtools/CigarContainsNoNOperator.md    |  2 +-
 docs/readtools/ComputeProperStatByWindow.md   |  2 +-
 docs/readtools/CutReadTrimmer.md              |  2 +-
 docs/readtools/DownloadDistmapResult.md       |  2 +-
 docs/readtools/FirstOfPairReadFilter.md       |  2 +-
 docs/readtools/FragmentLengthReadFilter.md    |  2 +-
 docs/readtools/GemMappabilityToBed.md         |  2 +-
 docs/readtools/GoodCigarReadFilter.md         |  2 +-
 docs/readtools/HasReadGroupReadFilter.md      |  2 +-
 docs/readtools/LibraryReadFilter.md           |  2 +-
 docs/readtools/MappedReadFilter.md            |  2 +-
 .../MappingQualityAvailableReadFilter.md      |  2 +-
 .../MappingQualityNotZeroReadFilter.md        |  2 +-
 docs/readtools/MappingQualityReadFilter.md    |  2 +-
 .../MatchingBasesAndQualsReadFilter.md        |  2 +-
 .../MateDifferentStrandReadFilter.md          |  2 +-
 ...ateOnSameContigOrNoMappedMateReadFilter.md |  2 +-
 docs/readtools/MetricsReadFilter.md           |  2 +-
 docs/readtools/MottQualityTrimmer.md          |  2 +-
 .../NonZeroFragmentLengthReadFilter.md        |  2 +-
 ...nZeroReferenceLengthAlignmentReadFilter.md |  2 +-
 docs/readtools/NotDuplicateReadFilter.md      |  2 +-
 .../NotSecondaryAlignmentReadFilter.md        |  2 +-
 .../NotSupplementaryAlignmentReadFilter.md    |  2 +-
 docs/readtools/OverclippedReadFilter.md       |  2 +-
 docs/readtools/PairedReadFilter.md            |  2 +-
 .../PassesVendorQualityCheckReadFilter.md     |  2 +-
 docs/readtools/PlatformReadFilter.md          |  2 +-
 docs/readtools/PlatformUnitReadFilter.md      |  2 +-
 docs/readtools/PrimaryLineReadFilter.md       |  2 +-
 docs/readtools/ProperlyPairedReadFilter.md    |  2 +-
 docs/readtools/QualityEncodingDetector.md     |  2 +-
 .../readtools/ReadGroupBlackListReadFilter.md |  2 +-
 docs/readtools/ReadGroupReadFilter.md         |  2 +-
 .../ReadLengthEqualsCigarLengthReadFilter.md  |  2 +-
 docs/readtools/ReadLengthReadFilter.md        |  2 +-
 docs/readtools/ReadNameReadFilter.md          |  2 +-
 docs/readtools/ReadStrandFilter.md            |  2 +-
 docs/readtools/ReadsToDistmap.md              |  2 +-
 docs/readtools/ReadsToFastq.md                |  2 +-
 docs/readtools/SampleReadFilter.md            |  2 +-
 docs/readtools/SecondOfPairReadFilter.md      |  2 +-
 docs/readtools/SeqIsStoredReadFilter.md       |  2 +-
 docs/readtools/StandardizeReads.md            |  2 +-
 docs/readtools/TrailingNtrimmer.md            |  2 +-
 docs/readtools/TrimReads.md                   |  2 +-
 docs/readtools/ValidAlignmentEndReadFilter.md |  2 +-
 .../ValidAlignmentStartReadFilter.md          |  2 +-
 docs/readtools/WellformedReadFilter.md        |  2 +-
 287 files changed, 1001 insertions(+), 951 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 17853683..c33c51fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,9 @@ The meaning of each entry is user-based and can be found in our
 
 ## [Unreleased]
 
+
+## [1.5.2]
+
 ### Fixed
 - Allow special characters in advance java-property for barcode sequence/quality separators
 
@@ -305,3 +308,4 @@ First pre-release
 [1.4.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.1
 [1.5.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.0
 [1.5.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.1
+[1.5.2]: https://github.com/magicDGS/ReadTools/releases/tag/1.5.2
diff --git a/docs/_data/index.yml b/docs/_data/index.yml
index 583e4ff0..da256ab9 100644
--- a/docs/_data/index.yml
+++ b/docs/_data/index.yml
@@ -1,6 +1,6 @@
 ReadTools:
-  version: 1.5.1
-  timestamp: 27-49-2018 03:49:16
+  version: 1.5.2
+  timestamp: 30-57-2018 12:57:55
 
 tools:
   - group: Diagnostics and Quality Control
diff --git a/docs/javadoc/allclasses-frame.html b/docs/javadoc/allclasses-frame.html
index 591c7be9..9a628451 100644
--- a/docs/javadoc/allclasses-frame.html
+++ b/docs/javadoc/allclasses-frame.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>All Classes (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>All Classes (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
diff --git a/docs/javadoc/allclasses-noframe.html b/docs/javadoc/allclasses-noframe.html
index 842708aa..fe3e2c09 100644
--- a/docs/javadoc/allclasses-noframe.html
+++ b/docs/javadoc/allclasses-noframe.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>All Classes (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>All Classes (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
diff --git a/docs/javadoc/constant-values.html b/docs/javadoc/constant-values.html
index 54592e6b..aed62cbf 100644
--- a/docs/javadoc/constant-values.html
+++ b/docs/javadoc/constant-values.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>Constant Field Values (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Constant Field Values (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Constant Field Values (ReadTools 1.5.1 API)";
+            parent.document.title="Constant Field Values (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/deprecated-list.html b/docs/javadoc/deprecated-list.html
index 4049dfc5..3f97025f 100644
--- a/docs/javadoc/deprecated-list.html
+++ b/docs/javadoc/deprecated-list.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>Deprecated List (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Deprecated List (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Deprecated List (ReadTools 1.5.1 API)";
+            parent.document.title="Deprecated List (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/help-doc.html b/docs/javadoc/help-doc.html
index 8e717213..56bf976e 100644
--- a/docs/javadoc/help-doc.html
+++ b/docs/javadoc/help-doc.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>API Help (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>API Help (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="API Help (ReadTools 1.5.1 API)";
+            parent.document.title="API Help (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/index-all.html b/docs/javadoc/index-all.html
index 050ed8eb..4cc7dadf 100644
--- a/docs/javadoc/index-all.html
+++ b/docs/javadoc/index-all.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>Index (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Index (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Index (ReadTools 1.5.1 API)";
+            parent.document.title="Index (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
@@ -479,6 +479,14 @@ <h2 class="title">D</h2>
 <dd>
 <div class="block">Decodes a single-end Distmap String.</div>
 </dd>
+<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT">DEFAULT_BARCODE_INDEX_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
+<dd>
+<div class="block">Default regular expression to split barcodes.</div>
+</dd>
+<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_QUALITY_SPLIT">DEFAULT_BARCODE_QUALITY_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
+<dd>
+<div class="block">Default regular expression to split barcode qualities.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html#DEFAULT_METRICS_EXTENSION">DEFAULT_METRICS_EXTENSION</a></span> - Static variable in interface org.magicdgs.readtools.utils.read.writer.<a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html" title="interface in org.magicdgs.readtools.utils.read.writer">ReadToolsIOFormat</a></dt>
 <dd>
 <div class="block">Output extension for metric files.</div>
@@ -667,7 +675,7 @@ <h2 class="title">E</h2>
 <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#extractBarcodesFromReadName-org.broadinstitute.hellbender.utils.read.GATKRead-">extractBarcodesFromReadName(GATKRead)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
 <dd>
 <div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name
- using <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>.</div>
+ using <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>.</div>
 </dd>
 </dl>
 <a name="I:F">
@@ -930,7 +938,7 @@ <h2 class="title">G</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html#getBarcodes-java.lang.String-">getBarcodes(String)</a></span> - Method in enum org.magicdgs.readtools.utils.fastq.<a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html" title="enum in org.magicdgs.readtools.utils.fastq">FastqReadNameEncoding</a></dt>
 <dd>
-<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>).</div>
+<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>).</div>
 </dd>
 <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#getBarcodesAndQualitiesFromTags-org.broadinstitute.hellbender.utils.read.GATKRead-java.util.List-java.util.List-">getBarcodesAndQualitiesFromTags(GATKRead, List&lt;String&gt;, List&lt;String&gt;)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt>
 <dd>
diff --git a/docs/javadoc/index.html b/docs/javadoc/index.html
index 709ececa..24ef86c4 100644
--- a/docs/javadoc/index.html
+++ b/docs/javadoc/index.html
@@ -2,8 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>ReadTools 1.5.1 API</title>
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>ReadTools 1.5.2 API</title>
 <script type="text/javascript">
     tmpTargetPage = "" + window.location.search;
     if (tmpTargetPage != "" && tmpTargetPage != "undefined")
diff --git a/docs/javadoc/org/magicdgs/readtools/Main.html b/docs/javadoc/org/magicdgs/readtools/Main.html
index a14bdb57..976788c8 100644
--- a/docs/javadoc/org/magicdgs/readtools/Main.html
+++ b/docs/javadoc/org/magicdgs/readtools/Main.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<title>Main (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>Main (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Main (ReadTools 1.5.1 API)";
+            parent.document.title="Main (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/RTDefaults.html b/docs/javadoc/org/magicdgs/readtools/RTDefaults.html
index a23821ee..f79d822b 100644
--- a/docs/javadoc/org/magicdgs/readtools/RTDefaults.html
+++ b/docs/javadoc/org/magicdgs/readtools/RTDefaults.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<title>RTDefaults (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>RTDefaults (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTDefaults (ReadTools 1.5.1 API)";
+            parent.document.title="RTDefaults (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html b/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html
index dea8f9ec..d4768448 100644
--- a/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html
+++ b/docs/javadoc/org/magicdgs/readtools/RTHelpConstants.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:07 GMT 2018 -->
-<title>RTHelpConstants (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>RTHelpConstants (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTHelpConstants (ReadTools 1.5.1 API)";
+            parent.document.title="RTHelpConstants (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html b/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html
index 706f4ab4..0873d41e 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/RTDeprecatedToolsRegistry.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTDeprecatedToolsRegistry (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>RTDeprecatedToolsRegistry (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTDeprecatedToolsRegistry (ReadTools 1.5.1 API)";
+            parent.document.title="RTDeprecatedToolsRegistry (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html b/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html
index 786047a2..36484445 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/RTStandardArguments.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTStandardArguments (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>RTStandardArguments (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTStandardArguments (ReadTools 1.5.1 API)";
+            parent.document.title="RTStandardArguments (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html
index 2113af77..a529399a 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/BarcodeDetectorArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>BarcodeDetectorArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>BarcodeDetectorArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="BarcodeDetectorArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="BarcodeDetectorArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html
index bf5877ab..694f7897 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection.FixBarcodeWithQualitiesArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html
index e03775f0..531f3415 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection.FixSimpleBarcodeArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html
index 7e74dfab..d13d1d0c 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/FixBarcodeAbstractArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>FixBarcodeAbstractArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>FixBarcodeAbstractArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="FixBarcodeAbstractArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="FixBarcodeAbstractArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTInputArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTInputArgumentCollection.html
index 962dab57..6af00c43 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTInputArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTInputArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTInputArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>RTInputArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTInputArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="RTInputArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputArgumentCollection.html
index 5799c9ad..2230a8a2 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTOutputArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>RTOutputArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTOutputArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="RTOutputArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamArgumentCollection.html
index 66782da6..c01f1c05 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTOutputBamArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>RTOutputBamArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="RTOutputBamArgumentCollection (ReadTools 1.5.1 API)";
+            parent.document.title="RTOutputBamArgumentCollection (ReadTools 1.5.2 API)";
         }
     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamSplitArgumentCollection.html b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamSplitArgumentCollection.html
index 502fb39c..85b7e9c9 100644
--- a/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamSplitArgumentCollection.html
+++ b/docs/javadoc/org/magicdgs/readtools/cmd/argumentcollections/RTOutputBamSplitArgumentCollection.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTOutputBamSplitArgumentCollection (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>RTOutputBamSplitArgumentCollection (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
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index 7887d0ec..5fc7276b 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.metrics (ReadTools 1.5.2 API)</title>
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index 4e768b7b..351138ae 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.metrics (ReadTools 1.5.2 API)</title>
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.metrics Class Hierarchy (ReadTools 1.5.2 API)</title>
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index c0a9273a..c098805a 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools (ReadTools 1.5.2 API)</title>
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index 796d53f2..2879b707 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools (ReadTools 1.5.2 API)</title>
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index c8bbf5a0..f3e3b3ed 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 224a845b..0a240444 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>AssignReadGroupByBarcode (ReadTools 1.5.2 API)</title>
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index c56dfd5a..b561c516 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>BarcodeDictionary (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 9f37bbe8..88f888e0 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>BarcodeDictionaryFactory (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>BarcodeDecoder (ReadTools 1.5.2 API)</title>
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>BarcodeMatch (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary.decoder (ReadTools 1.5.2 API)</title>
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary.decoder (ReadTools 1.5.2 API)</title>
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary.decoder Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../script.js"></script>
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>org.magicdgs.readtools.tools.barcodes.dictionary Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>FastqGATKWriter (ReadTools 1.5.2 API)</title>
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html b/docs/javadoc/org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>FastqReadNameEncoding (ReadTools 1.5.2 API)</title>
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@@ -164,7 +164,7 @@ <h3>Method Summary</h3>
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+<div class="block">Returns the barcodes in the read name (splitted by <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>).</div>
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+<div class="block">Returns the barcodes in the read name (splitted by <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>).</div>
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+<title>org.magicdgs.readtools.utils.math (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/math/package-tree.html b/docs/javadoc/org/magicdgs/readtools/utils/math/package-tree.html
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:09 GMT 2018 -->
-<title>org.magicdgs.readtools.utils.math Class Hierarchy (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.math Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/package-summary.html b/docs/javadoc/org/magicdgs/readtools/utils/package-summary.html
index a28e0b21..32344c07 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/RTReadUtils.html b/docs/javadoc/org/magicdgs/readtools/utils/read/RTReadUtils.html
index 64e3d8f0..db1b64a8 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>RTReadUtils (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>RTReadUtils (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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@@ -12,7 +12,7 @@
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@@ -130,6 +130,18 @@ <h3>Field Summary</h3>
 <th class="colLast" scope="col">Field and Description</th>
 </tr>
 <tr class="altColor">
+<td class="colFirst"><code>static java.util.regex.Pattern</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT">DEFAULT_BARCODE_INDEX_SPLIT</a></span></code>
+<div class="block">Default regular expression to split barcodes.</div>
+</td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><code>static java.util.regex.Pattern</code></td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_QUALITY_SPLIT">DEFAULT_BARCODE_QUALITY_SPLIT</a></span></code>
+<div class="block">Default regular expression to split barcode qualities.</div>
+</td>
+</tr>
+<tr class="altColor">
 <td class="colFirst"><code>static java.lang.String</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#RAW_BARCODE_QUALITY_TAG">RAW_BARCODE_QUALITY_TAG</a></span></code>
 <div class="block">Default raw barcode tag for qualities (as defined in the SAM specs).</div>
@@ -195,7 +207,7 @@ <h3>Method Summary</h3>
 <td class="colFirst"><code>static java.lang.String[]</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#extractBarcodesFromReadName-org.broadinstitute.hellbender.utils.read.GATKRead-">extractBarcodesFromReadName</a></span>(org.broadinstitute.hellbender.utils.read.GATKRead&nbsp;read)</code>
 <div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name
- using <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>.</div>
+ using <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>DEFAULT_BARCODE_INDEX_SPLIT</code></a>.</div>
 </td>
 </tr>
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@@ -349,13 +361,39 @@ <h4>RAW_BARCODE_QUALITY_TAG</h4>
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 <h4>RAW_BARCODE_TAG_LIST</h4>
 <pre>public static final&nbsp;java.util.List&lt;java.lang.String&gt; RAW_BARCODE_TAG_LIST</pre>
 <div class="block">Default raw barcode tag (<a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#RAW_BARCODE_TAG"><code>RAW_BARCODE_TAG</code></a>) as a singleton list.</div>
 </li>
 </ul>
+<a name="DEFAULT_BARCODE_INDEX_SPLIT">
+<!--   -->
+</a>
+<ul class="blockList">
+<li class="blockList">
+<h4>DEFAULT_BARCODE_INDEX_SPLIT</h4>
+<pre>public static final&nbsp;java.util.regex.Pattern DEFAULT_BARCODE_INDEX_SPLIT</pre>
+<div class="block">Default regular expression to split barcodes.
+
+ <p>Uses a quoted <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a> to allow string representation
+ in the java-property.</div>
+</li>
+</ul>
+<a name="DEFAULT_BARCODE_QUALITY_SPLIT">
+<!--   -->
+</a>
+<ul class="blockListLast">
+<li class="blockList">
+<h4>DEFAULT_BARCODE_QUALITY_SPLIT</h4>
+<pre>public static final&nbsp;java.util.regex.Pattern DEFAULT_BARCODE_QUALITY_SPLIT</pre>
+<div class="block">Default regular expression to split barcode qualities.
+
+ <p>Uses a quoted <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_QUALITY_DELIMITER"><code>RTDefaults.BARCODE_QUALITY_DELIMITER</code></a> to allow string representation
+ in the java-property.</div>
+</li>
+</ul>
 </li>
 </ul>
 <!-- ============ METHOD DETAIL ========== -->
@@ -372,7 +410,7 @@ <h3>Method Detail</h3>
 <h4>extractBarcodesFromReadName</h4>
 <pre>public static&nbsp;java.lang.String[]&nbsp;extractBarcodesFromReadName(org.broadinstitute.hellbender.utils.read.GATKRead&nbsp;read)</pre>
 <div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name
- using <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>. The read will
+ using <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>DEFAULT_BARCODE_INDEX_SPLIT</code></a>. The read will
 
  The barcode should be encoded in the Illumina format (not pair-end information included),
  for example (barcode delimiter in the example is the default):
@@ -395,7 +433,7 @@ <h4>getBarcodesFromTags</h4>
 <pre>public static&nbsp;java.lang.String[]&nbsp;getBarcodesFromTags(org.broadinstitute.hellbender.utils.read.GATKRead&nbsp;read,
                                                      java.util.List&lt;java.lang.String&gt;&nbsp;tags)</pre>
 <div class="block">Returns an array that contains the barcodes stored in the provided tags. The tags are
- splitted by <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a> to check if there are more than 1
+ splitted by <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>DEFAULT_BARCODE_INDEX_SPLIT</code></a> to check if there are more than 1
  sequence. If the value for a tag is <code>null</code> (does not exists), this tag is skipped.
 
  Note: no validation is performed to check if the tags are real barcodes.</div>
@@ -420,13 +458,13 @@ <h4>getBarcodesAndQualitiesFromTags</h4>
                                                                                                                          java.util.List&lt;java.lang.String&gt;&nbsp;barcodeTags,
                                                                                                                          java.util.List&lt;java.lang.String&gt;&nbsp;qualityTags)</pre>
 <div class="block">Returns an pair of arrays of the same length that contains the barcodes/qualities stored in
- the provided tags. The tags are splitted by <a href="../../../../../org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a> to
+ the provided tags. The tags are splitted by <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>DEFAULT_BARCODE_INDEX_SPLIT</code></a> to
  check if there are more than 1 sequence/quality. If the value for a tag is <code>null</code>
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  is empty for the corresponding tag, the quality is filled with <a href="../../../../../org/magicdgs/readtools/utils/read/RTReadUtils.html#ZERO_QUALITY_CHAR"><code>ZERO_QUALITY_CHAR</code></a> to
  match the same length.
 
- Note: no validation is performed to check if the tags are real barcodes/qualities.</div>
+ <p>Note: no validation is performed to check if the tags are real barcodes/qualities.</div>
 <dl>
 <dt><span class="paramLabel">Parameters:</span></dt>
 <dd><code>read</code> - the read to extract the barcodes from.</dd>
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>ReadReaderFactory (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>ReadWriterFactory (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/ReservedTags.html b/docs/javadoc/org/magicdgs/readtools/utils/read/ReservedTags.html
index 32872ed6..01991af2 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/read/ReservedTags.html
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@@ -2,9 +2,9 @@
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>ReservedTags (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>ReservedTags (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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@@ -12,7 +12,7 @@
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-            parent.document.title="ReservedTags (ReadTools 1.5.1 API)";
+            parent.document.title="ReservedTags (ReadTools 1.5.2 API)";
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/filter/CompletelyTrimReadFilter.html b/docs/javadoc/org/magicdgs/readtools/utils/read/filter/CompletelyTrimReadFilter.html
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>CompletelyTrimReadFilter (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/filter/package-frame.html b/docs/javadoc/org/magicdgs/readtools/utils/read/filter/package-frame.html
index 6bbab76e..6247c39c 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.filter (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.filter (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.filter Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
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index ff27493c..86dfdb33 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.stats.pairstat (ReadTools 1.5.2 API)</title>
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/stats/pairstat/package-tree.html b/docs/javadoc/org/magicdgs/readtools/utils/read/stats/pairstat/package-tree.html
index aafd6b45..2884116c 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.stats.pairstat Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 53a215df..bb535b17 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>ContainIndelCounter (ReadTools 1.5.2 API)</title>
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index 354acbca..7a1c096b 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/read/stats/singlestat/ContainSoftclipCounter.html
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>ContainSoftclipCounter (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 2c20eb90..1faf76d3 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.stats.singlestat (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/stats/singlestat/package-summary.html b/docs/javadoc/org/magicdgs/readtools/utils/read/stats/singlestat/package-summary.html
index a68a97be..2b213bd2 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/read/stats/singlestat/package-summary.html
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.stats.singlestat (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index c9ba6181..aa2408bb 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.stats.singlestat Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 108ed478..b95c28fb 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:43 GMT 2018 -->
+<title>CheckQualityReadTransformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 9cb2438b..fdd00178 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:43 GMT 2018 -->
+<title>SolexaToSangerReadTransformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 475ad665..ab0f9a17 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>FixRawBarcodeTagsReadTransformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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index 4d7e2397..95f7b573 100644
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-<title>FixReadNameBarcodesReadTransformer (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:44 GMT 2018 -->
+<title>FixReadNameBarcodesReadTransformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
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index 5c82dcec..ee118bf2 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.transformer.barcodes (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../../script.js"></script>
 </head>
diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/barcodes/package-summary.html b/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/barcodes/package-summary.html
index 6f88ab75..6a8600f0 100644
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>org.magicdgs.readtools.utils.read.transformer.barcodes (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.transformer.barcodes (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../../script.js"></script>
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index dcc95373..39f56f25 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/barcodes/package-tree.html
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-<title>org.magicdgs.readtools.utils.read.transformer.barcodes Class Hierarchy (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.transformer.barcodes Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../../script.js"></script>
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+            parent.document.title="org.magicdgs.readtools.utils.read.transformer.barcodes Class Hierarchy (ReadTools 1.5.2 API)";
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-frame.html b/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-frame.html
index 696f85dd..1ca9b83a 100644
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-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.transformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../script.js"></script>
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-summary.html b/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-summary.html
index b81ec502..36c49d75 100644
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-<title>org.magicdgs.readtools.utils.read.transformer (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.transformer (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-tree.html b/docs/javadoc/org/magicdgs/readtools/utils/read/transformer/package-tree.html
index 6c79af74..e1548a02 100644
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
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@@ -2,9 +2,9 @@
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 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>org.magicdgs.readtools.utils.read.writer Class Hierarchy (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.read.writer Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../../script.js"></script>
 </head>
@@ -12,7 +12,7 @@
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         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="org.magicdgs.readtools.utils.read.writer Class Hierarchy (ReadTools 1.5.1 API)";
+            parent.document.title="org.magicdgs.readtools.utils.read.writer Class Hierarchy (ReadTools 1.5.2 API)";
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     catch(err) {
@@ -100,8 +100,8 @@ <h2 title="Enum Hierarchy">Enum Hierarchy</h2>
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 <li type="circle">org.magicdgs.readtools.utils.read.writer.<a href="../../../../../../org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.BamFormat.html" title="enum in org.magicdgs.readtools.utils.read.writer"><span class="typeNameLink">ReadToolsIOFormat.BamFormat</span></a> (implements org.magicdgs.readtools.utils.read.writer.<a href="../../../../../../org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html" title="interface in org.magicdgs.readtools.utils.read.writer">ReadToolsIOFormat</a>)</li>
+<li type="circle">org.magicdgs.readtools.utils.read.writer.<a href="../../../../../../org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.FastqFormat.html" title="enum in org.magicdgs.readtools.utils.read.writer"><span class="typeNameLink">ReadToolsIOFormat.FastqFormat</span></a> (implements org.magicdgs.readtools.utils.read.writer.<a href="../../../../../../org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html" title="interface in org.magicdgs.readtools.utils.read.writer">ReadToolsIOFormat</a>)</li>
 </ul>
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html b/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html
index 4bebd570..57001edb 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html
+++ b/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimAndFilterPipeline.html
@@ -2,9 +2,9 @@
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-<title>TrimAndFilterPipeline (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>TrimAndFilterPipeline (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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 <script type="text/javascript" src="../../../../../script.js"></script>
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@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="TrimAndFilterPipeline (ReadTools 1.5.1 API)";
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     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimmingUtil.html b/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimmingUtil.html
index fef95449..127ab5e8 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimmingUtil.html
+++ b/docs/javadoc/org/magicdgs/readtools/utils/trimming/TrimmingUtil.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:08 GMT 2018 -->
-<title>TrimmingUtil (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:45 GMT 2018 -->
+<title>TrimmingUtil (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
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@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
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-            parent.document.title="TrimmingUtil (ReadTools 1.5.1 API)";
+            parent.document.title="TrimmingUtil (ReadTools 1.5.2 API)";
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     }
     catch(err) {
diff --git a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-frame.html b/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-frame.html
index cea9e2c0..4e0a71ef 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-frame.html
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@@ -2,9 +2,9 @@
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-<title>org.magicdgs.readtools.utils.trimming (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.trimming (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
 <script type="text/javascript" src="../../../../../script.js"></script>
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-summary.html b/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-summary.html
index 1287de51..23267fb6 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-summary.html
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@@ -2,9 +2,9 @@
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-<title>org.magicdgs.readtools.utils.trimming (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.trimming (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="../../../../../stylesheet.css" title="Style">
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@@ -12,7 +12,7 @@
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+            parent.document.title="org.magicdgs.readtools.utils.trimming (ReadTools 1.5.2 API)";
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diff --git a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-tree.html b/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-tree.html
index b64ed6fe..103bd320 100644
--- a/docs/javadoc/org/magicdgs/readtools/utils/trimming/package-tree.html
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@@ -2,9 +2,9 @@
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-<title>org.magicdgs.readtools.utils.trimming Class Hierarchy (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>org.magicdgs.readtools.utils.trimming Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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@@ -12,7 +12,7 @@
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-            parent.document.title="org.magicdgs.readtools.utils.trimming Class Hierarchy (ReadTools 1.5.1 API)";
+            parent.document.title="org.magicdgs.readtools.utils.trimming Class Hierarchy (ReadTools 1.5.2 API)";
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diff --git a/docs/javadoc/overview-frame.html b/docs/javadoc/overview-frame.html
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@@ -2,9 +2,9 @@
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-<title>Overview List (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:46 GMT 2018 -->
+<title>Overview List (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
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diff --git a/docs/javadoc/overview-summary.html b/docs/javadoc/overview-summary.html
index 88893891..d6d81938 100644
--- a/docs/javadoc/overview-summary.html
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
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-<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 -->
-<title>Overview (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Overview (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Overview (ReadTools 1.5.1 API)";
+            parent.document.title="Overview (ReadTools 1.5.2 API)";
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@@ -69,7 +69,7 @@
 </a></div>
 <!-- ========= END OF TOP NAVBAR ========= -->
 <div class="header">
-<h1 class="title">ReadTools 1.5.1 API</h1>
+<h1 class="title">ReadTools 1.5.2 API</h1>
 </div>
 <div class="contentContainer">
 <table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Packages table, listing packages, and an explanation">
diff --git a/docs/javadoc/overview-tree.html b/docs/javadoc/overview-tree.html
index bc001f20..3c74b0a4 100644
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 <!-- NewPage -->
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-<title>Class Hierarchy (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Class Hierarchy (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
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@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Class Hierarchy (ReadTools 1.5.1 API)";
+            parent.document.title="Class Hierarchy (ReadTools 1.5.2 API)";
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diff --git a/docs/javadoc/serialized-form.html b/docs/javadoc/serialized-form.html
index 881d5061..8b2b9133 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
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-<title>Serialized Form (ReadTools 1.5.1 API)</title>
-<meta name="date" content="2018-08-27">
+<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 -->
+<title>Serialized Form (ReadTools 1.5.2 API)</title>
+<meta name="date" content="2018-08-30">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
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@@ -12,7 +12,7 @@
 <script type="text/javascript"><!--
     try {
         if (location.href.indexOf('is-external=true') == -1) {
-            parent.document.title="Serialized Form (ReadTools 1.5.1 API)";
+            parent.document.title="Serialized Form (ReadTools 1.5.2 API)";
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diff --git a/docs/readtools/AlignmentAgreesWithHeaderReadFilter.md b/docs/readtools/AlignmentAgreesWithHeaderReadFilter.md
index 1cd31ce1..57ffadca 100644
--- a/docs/readtools/AlignmentAgreesWithHeaderReadFilter.md
+++ b/docs/readtools/AlignmentAgreesWithHeaderReadFilter.md
@@ -2,7 +2,7 @@
 title: AlignmentAgreesWithHeaderReadFilter
 summary: Filters out reads where the alignment does not match the contents of the header
 permalink: AlignmentAgreesWithHeaderReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/AllowAllReadsReadFilter.md b/docs/readtools/AllowAllReadsReadFilter.md
index a0edc720..84ff0394 100644
--- a/docs/readtools/AllowAllReadsReadFilter.md
+++ b/docs/readtools/AllowAllReadsReadFilter.md
@@ -2,7 +2,7 @@
 title: AllowAllReadsReadFilter
 summary: Do not filter out any read
 permalink: AllowAllReadsReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/AmbiguousBaseReadFilter.md b/docs/readtools/AmbiguousBaseReadFilter.md
index 8bc09991..e3725715 100644
--- a/docs/readtools/AmbiguousBaseReadFilter.md
+++ b/docs/readtools/AmbiguousBaseReadFilter.md
@@ -2,7 +2,7 @@
 title: AmbiguousBaseReadFilter
 summary: Filters out reads that have greater than the threshold number of N bases
 permalink: AmbiguousBaseReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/AssignReadGroupByBarcode.md b/docs/readtools/AssignReadGroupByBarcode.md
index 453c8d3d..ca1001ec 100644
--- a/docs/readtools/AssignReadGroupByBarcode.md
+++ b/docs/readtools/AssignReadGroupByBarcode.md
@@ -2,7 +2,7 @@
 title: AssignReadGroupByBarcode
 summary: Assigns read groups based on barcode tag(s) for all kind of sources for ReadTools.
 permalink: AssignReadGroupByBarcode.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/CigarContainsNoNOperator.md b/docs/readtools/CigarContainsNoNOperator.md
index 16beecb7..8b058582 100644
--- a/docs/readtools/CigarContainsNoNOperator.md
+++ b/docs/readtools/CigarContainsNoNOperator.md
@@ -2,7 +2,7 @@
 title: CigarContainsNoNOperator
 summary: Filter out reads with CIGAR containing N operator
 permalink: CigarContainsNoNOperator.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ComputeProperStatByWindow.md b/docs/readtools/ComputeProperStatByWindow.md
index c394210c..05692b52 100644
--- a/docs/readtools/ComputeProperStatByWindow.md
+++ b/docs/readtools/ComputeProperStatByWindow.md
@@ -2,7 +2,7 @@
 title: ComputeProperStatByWindow (EXPERIMENTAL)
 summary: Computes proper-paired reads statistics over windows 
 permalink: ComputeProperStatByWindow.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 {% include warning.html content="This a EXPERIMENTAL tool and should not be used for production" %}
diff --git a/docs/readtools/CutReadTrimmer.md b/docs/readtools/CutReadTrimmer.md
index feb6db05..9d4f07bc 100644
--- a/docs/readtools/CutReadTrimmer.md
+++ b/docs/readtools/CutReadTrimmer.md
@@ -2,7 +2,7 @@
 title: CutReadTrimmer
 summary: Crops a concrete number of bases at the end of the read.
 permalink: CutReadTrimmer.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/DownloadDistmapResult.md b/docs/readtools/DownloadDistmapResult.md
index 0c884c09..4e2bb99c 100644
--- a/docs/readtools/DownloadDistmapResult.md
+++ b/docs/readtools/DownloadDistmapResult.md
@@ -2,7 +2,7 @@
 title: DownloadDistmapResult
 summary: Download, sort and merge the alignments generated by DistMap.
 permalink: DownloadDistmapResult.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/FirstOfPairReadFilter.md b/docs/readtools/FirstOfPairReadFilter.md
index 977a9c94..b3801a40 100644
--- a/docs/readtools/FirstOfPairReadFilter.md
+++ b/docs/readtools/FirstOfPairReadFilter.md
@@ -2,7 +2,7 @@
 title: FirstOfPairReadFilter
 summary: Keep only reads that are first of pair
 permalink: FirstOfPairReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/FragmentLengthReadFilter.md b/docs/readtools/FragmentLengthReadFilter.md
index 59aa18a2..4754746b 100644
--- a/docs/readtools/FragmentLengthReadFilter.md
+++ b/docs/readtools/FragmentLengthReadFilter.md
@@ -2,7 +2,7 @@
 title: FragmentLengthReadFilter
 summary: Keep only read pairs with insert length less than or equal to the given value
 permalink: FragmentLengthReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/GemMappabilityToBed.md b/docs/readtools/GemMappabilityToBed.md
index 367fef22..0df066d6 100644
--- a/docs/readtools/GemMappabilityToBed.md
+++ b/docs/readtools/GemMappabilityToBed.md
@@ -2,7 +2,7 @@
 title: GemMappabilityToBed (EXPERIMENTAL)
 summary: Converts a GEM-mappability file into a BED-graph format
 permalink: GemMappabilityToBed.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 {% include warning.html content="This a EXPERIMENTAL tool and should not be used for production" %}
diff --git a/docs/readtools/GoodCigarReadFilter.md b/docs/readtools/GoodCigarReadFilter.md
index 108117d0..faf97832 100644
--- a/docs/readtools/GoodCigarReadFilter.md
+++ b/docs/readtools/GoodCigarReadFilter.md
@@ -2,7 +2,7 @@
 title: GoodCigarReadFilter
 summary: Keep only reads containing good CIGAR string
 permalink: GoodCigarReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/HasReadGroupReadFilter.md b/docs/readtools/HasReadGroupReadFilter.md
index 5f24d719..5d21761e 100644
--- a/docs/readtools/HasReadGroupReadFilter.md
+++ b/docs/readtools/HasReadGroupReadFilter.md
@@ -2,7 +2,7 @@
 title: HasReadGroupReadFilter
 summary: Filter out reads without Read Group
 permalink: HasReadGroupReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/LibraryReadFilter.md b/docs/readtools/LibraryReadFilter.md
index f9e90803..f4a7b965 100644
--- a/docs/readtools/LibraryReadFilter.md
+++ b/docs/readtools/LibraryReadFilter.md
@@ -2,7 +2,7 @@
 title: LibraryReadFilter
 summary: Keep only reads from the specified library
 permalink: LibraryReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MappedReadFilter.md b/docs/readtools/MappedReadFilter.md
index f33c03d3..dc0b8045 100644
--- a/docs/readtools/MappedReadFilter.md
+++ b/docs/readtools/MappedReadFilter.md
@@ -2,7 +2,7 @@
 title: MappedReadFilter
 summary: Filter out unmapped reads
 permalink: MappedReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MappingQualityAvailableReadFilter.md b/docs/readtools/MappingQualityAvailableReadFilter.md
index add1f5ad..6d98d5b1 100644
--- a/docs/readtools/MappingQualityAvailableReadFilter.md
+++ b/docs/readtools/MappingQualityAvailableReadFilter.md
@@ -2,7 +2,7 @@
 title: MappingQualityAvailableReadFilter
 summary: Filter out reads without available mapping quality
 permalink: MappingQualityAvailableReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MappingQualityNotZeroReadFilter.md b/docs/readtools/MappingQualityNotZeroReadFilter.md
index b145dba6..054aa54e 100644
--- a/docs/readtools/MappingQualityNotZeroReadFilter.md
+++ b/docs/readtools/MappingQualityNotZeroReadFilter.md
@@ -2,7 +2,7 @@
 title: MappingQualityNotZeroReadFilter
 summary: Filter out reads with mapping quality equal to zero
 permalink: MappingQualityNotZeroReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MappingQualityReadFilter.md b/docs/readtools/MappingQualityReadFilter.md
index bb05db97..68f51023 100644
--- a/docs/readtools/MappingQualityReadFilter.md
+++ b/docs/readtools/MappingQualityReadFilter.md
@@ -2,7 +2,7 @@
 title: MappingQualityReadFilter
 summary: Keep only reads with mapping qualities within a specified range
 permalink: MappingQualityReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MatchingBasesAndQualsReadFilter.md b/docs/readtools/MatchingBasesAndQualsReadFilter.md
index 70eeff76..cd645463 100644
--- a/docs/readtools/MatchingBasesAndQualsReadFilter.md
+++ b/docs/readtools/MatchingBasesAndQualsReadFilter.md
@@ -2,7 +2,7 @@
 title: MatchingBasesAndQualsReadFilter
 summary: Filter out reads where the bases and qualities do not match
 permalink: MatchingBasesAndQualsReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MateDifferentStrandReadFilter.md b/docs/readtools/MateDifferentStrandReadFilter.md
index 8fa0756f..79f0b257 100644
--- a/docs/readtools/MateDifferentStrandReadFilter.md
+++ b/docs/readtools/MateDifferentStrandReadFilter.md
@@ -2,7 +2,7 @@
 title: MateDifferentStrandReadFilter
 summary: Keep only reads with mates mapped on the different strand
 permalink: MateDifferentStrandReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MateOnSameContigOrNoMappedMateReadFilter.md b/docs/readtools/MateOnSameContigOrNoMappedMateReadFilter.md
index 10aecf75..ddc0036e 100644
--- a/docs/readtools/MateOnSameContigOrNoMappedMateReadFilter.md
+++ b/docs/readtools/MateOnSameContigOrNoMappedMateReadFilter.md
@@ -2,7 +2,7 @@
 title: MateOnSameContigOrNoMappedMateReadFilter
 summary: Keep only reads whose mate maps to the same contig or is unmapped
 permalink: MateOnSameContigOrNoMappedMateReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MetricsReadFilter.md b/docs/readtools/MetricsReadFilter.md
index 627a18c1..feac5bca 100644
--- a/docs/readtools/MetricsReadFilter.md
+++ b/docs/readtools/MetricsReadFilter.md
@@ -2,7 +2,7 @@
 title: MetricsReadFilter
 summary: Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments
 permalink: MetricsReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/MottQualityTrimmer.md b/docs/readtools/MottQualityTrimmer.md
index 390405ad..ea9edbda 100644
--- a/docs/readtools/MottQualityTrimmer.md
+++ b/docs/readtools/MottQualityTrimmer.md
@@ -2,7 +2,7 @@
 title: MottQualityTrimmer
 summary: Trims low quality ends using the Mott's algorithm.
 permalink: MottQualityTrimmer.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/NonZeroFragmentLengthReadFilter.md b/docs/readtools/NonZeroFragmentLengthReadFilter.md
index fb0c9365..a9318dda 100644
--- a/docs/readtools/NonZeroFragmentLengthReadFilter.md
+++ b/docs/readtools/NonZeroFragmentLengthReadFilter.md
@@ -2,7 +2,7 @@
 title: NonZeroFragmentLengthReadFilter
 summary: Filter out reads with fragment length different from zero
 permalink: NonZeroFragmentLengthReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/NonZeroReferenceLengthAlignmentReadFilter.md b/docs/readtools/NonZeroReferenceLengthAlignmentReadFilter.md
index 63620512..2699cab4 100644
--- a/docs/readtools/NonZeroReferenceLengthAlignmentReadFilter.md
+++ b/docs/readtools/NonZeroReferenceLengthAlignmentReadFilter.md
@@ -2,7 +2,7 @@
 title: NonZeroReferenceLengthAlignmentReadFilter
 summary: Filter out reads that do not align to the reference
 permalink: NonZeroReferenceLengthAlignmentReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/NotDuplicateReadFilter.md b/docs/readtools/NotDuplicateReadFilter.md
index 544154f9..1e2ddbe9 100644
--- a/docs/readtools/NotDuplicateReadFilter.md
+++ b/docs/readtools/NotDuplicateReadFilter.md
@@ -2,7 +2,7 @@
 title: NotDuplicateReadFilter
 summary: Filter out reads marked as duplicate
 permalink: NotDuplicateReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/NotSecondaryAlignmentReadFilter.md b/docs/readtools/NotSecondaryAlignmentReadFilter.md
index a2031f2e..f313d1e3 100644
--- a/docs/readtools/NotSecondaryAlignmentReadFilter.md
+++ b/docs/readtools/NotSecondaryAlignmentReadFilter.md
@@ -2,7 +2,7 @@
 title: NotSecondaryAlignmentReadFilter
 summary: Filter out reads representing secondary alignments
 permalink: NotSecondaryAlignmentReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/NotSupplementaryAlignmentReadFilter.md b/docs/readtools/NotSupplementaryAlignmentReadFilter.md
index b2defc90..f5ffe597 100644
--- a/docs/readtools/NotSupplementaryAlignmentReadFilter.md
+++ b/docs/readtools/NotSupplementaryAlignmentReadFilter.md
@@ -2,7 +2,7 @@
 title: NotSupplementaryAlignmentReadFilter
 summary: Filter out reads representing supplementary alignments
 permalink: NotSupplementaryAlignmentReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/OverclippedReadFilter.md b/docs/readtools/OverclippedReadFilter.md
index 95516856..99c0761d 100644
--- a/docs/readtools/OverclippedReadFilter.md
+++ b/docs/readtools/OverclippedReadFilter.md
@@ -2,7 +2,7 @@
 title: OverclippedReadFilter
 summary: Filter out reads that are over-soft-clipped
 permalink: OverclippedReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/PairedReadFilter.md b/docs/readtools/PairedReadFilter.md
index 21bb653c..7f23da1a 100644
--- a/docs/readtools/PairedReadFilter.md
+++ b/docs/readtools/PairedReadFilter.md
@@ -2,7 +2,7 @@
 title: PairedReadFilter
 summary: Filter out unpaired reads
 permalink: PairedReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/PassesVendorQualityCheckReadFilter.md b/docs/readtools/PassesVendorQualityCheckReadFilter.md
index 9b051b1e..97d851de 100644
--- a/docs/readtools/PassesVendorQualityCheckReadFilter.md
+++ b/docs/readtools/PassesVendorQualityCheckReadFilter.md
@@ -2,7 +2,7 @@
 title: PassesVendorQualityCheckReadFilter
 summary: Filter out reads failing platfor/vendor quality checks
 permalink: PassesVendorQualityCheckReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/PlatformReadFilter.md b/docs/readtools/PlatformReadFilter.md
index 3ecbe43b..01686cdd 100644
--- a/docs/readtools/PlatformReadFilter.md
+++ b/docs/readtools/PlatformReadFilter.md
@@ -2,7 +2,7 @@
 title: PlatformReadFilter
 summary: Keep only reads with matching Read Group platform
 permalink: PlatformReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/PlatformUnitReadFilter.md b/docs/readtools/PlatformUnitReadFilter.md
index 7efbb468..2350672a 100644
--- a/docs/readtools/PlatformUnitReadFilter.md
+++ b/docs/readtools/PlatformUnitReadFilter.md
@@ -2,7 +2,7 @@
 title: PlatformUnitReadFilter
 summary: Filter out reads with matching platform unit attribute
 permalink: PlatformUnitReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/PrimaryLineReadFilter.md b/docs/readtools/PrimaryLineReadFilter.md
index 72a3ab02..38aaf57d 100644
--- a/docs/readtools/PrimaryLineReadFilter.md
+++ b/docs/readtools/PrimaryLineReadFilter.md
@@ -4,7 +4,7 @@ summary: Keep only reads representing primary alignments (those that satisfy bot
  NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or
  0x800 flags set).
 permalink: PrimaryLineReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ProperlyPairedReadFilter.md b/docs/readtools/ProperlyPairedReadFilter.md
index 0a805070..de4916fa 100644
--- a/docs/readtools/ProperlyPairedReadFilter.md
+++ b/docs/readtools/ProperlyPairedReadFilter.md
@@ -2,7 +2,7 @@
 title: ProperlyPairedReadFilter
 summary: Keep only reads that are properly paired
 permalink: ProperlyPairedReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/QualityEncodingDetector.md b/docs/readtools/QualityEncodingDetector.md
index 45fef89e..418818bd 100644
--- a/docs/readtools/QualityEncodingDetector.md
+++ b/docs/readtools/QualityEncodingDetector.md
@@ -2,7 +2,7 @@
 title: QualityEncodingDetector
 summary: Detects the quality encoding format for all kind of sources for ReadTools.
 permalink: QualityEncodingDetector.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadGroupBlackListReadFilter.md b/docs/readtools/ReadGroupBlackListReadFilter.md
index 46226f3c..d6763494 100644
--- a/docs/readtools/ReadGroupBlackListReadFilter.md
+++ b/docs/readtools/ReadGroupBlackListReadFilter.md
@@ -2,7 +2,7 @@
 title: ReadGroupBlackListReadFilter
 summary: Keep records not matching the read group tag and exact match string.
 permalink: ReadGroupBlackListReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadGroupReadFilter.md b/docs/readtools/ReadGroupReadFilter.md
index efa4fd98..01875f05 100644
--- a/docs/readtools/ReadGroupReadFilter.md
+++ b/docs/readtools/ReadGroupReadFilter.md
@@ -2,7 +2,7 @@
 title: ReadGroupReadFilter
 summary: Keep only reads from the specified read group
 permalink: ReadGroupReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadLengthEqualsCigarLengthReadFilter.md b/docs/readtools/ReadLengthEqualsCigarLengthReadFilter.md
index dcb82343..aa2c08e0 100644
--- a/docs/readtools/ReadLengthEqualsCigarLengthReadFilter.md
+++ b/docs/readtools/ReadLengthEqualsCigarLengthReadFilter.md
@@ -2,7 +2,7 @@
 title: ReadLengthEqualsCigarLengthReadFilter
 summary: Filter out reads  where the read and CIGAR do not match in length
 permalink: ReadLengthEqualsCigarLengthReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadLengthReadFilter.md b/docs/readtools/ReadLengthReadFilter.md
index 69c2c511..5901fda1 100644
--- a/docs/readtools/ReadLengthReadFilter.md
+++ b/docs/readtools/ReadLengthReadFilter.md
@@ -2,7 +2,7 @@
 title: ReadLengthReadFilter
 summary: Keep only reads whose length is within a certain range
 permalink: ReadLengthReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadNameReadFilter.md b/docs/readtools/ReadNameReadFilter.md
index 9fddf8d9..19a831a6 100644
--- a/docs/readtools/ReadNameReadFilter.md
+++ b/docs/readtools/ReadNameReadFilter.md
@@ -2,7 +2,7 @@
 title: ReadNameReadFilter
 summary: Keep only reads with this read name
 permalink: ReadNameReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadStrandFilter.md b/docs/readtools/ReadStrandFilter.md
index defea9bb..4ccb2a77 100644
--- a/docs/readtools/ReadStrandFilter.md
+++ b/docs/readtools/ReadStrandFilter.md
@@ -2,7 +2,7 @@
 title: ReadStrandFilter
 summary: Keep only reads whose strand is as specified
 permalink: ReadStrandFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadsToDistmap.md b/docs/readtools/ReadsToDistmap.md
index 8f9fc9eb..d08248d2 100644
--- a/docs/readtools/ReadsToDistmap.md
+++ b/docs/readtools/ReadsToDistmap.md
@@ -2,7 +2,7 @@
 title: ReadsToDistmap
 summary: Converts any kind of ReadTools source to Distmap format.
 permalink: ReadsToDistmap.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ReadsToFastq.md b/docs/readtools/ReadsToFastq.md
index 0f2031ad..9c6727cd 100644
--- a/docs/readtools/ReadsToFastq.md
+++ b/docs/readtools/ReadsToFastq.md
@@ -2,7 +2,7 @@
 title: ReadsToFastq
 summary: Converts any kind of ReadTools source to FASTQ format.
 permalink: ReadsToFastq.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/SampleReadFilter.md b/docs/readtools/SampleReadFilter.md
index d5cb3fcf..576547b5 100644
--- a/docs/readtools/SampleReadFilter.md
+++ b/docs/readtools/SampleReadFilter.md
@@ -2,7 +2,7 @@
 title: SampleReadFilter
 summary: Keep only reads for a given sample
 permalink: SampleReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/SecondOfPairReadFilter.md b/docs/readtools/SecondOfPairReadFilter.md
index ab72ee00..9f3185e3 100644
--- a/docs/readtools/SecondOfPairReadFilter.md
+++ b/docs/readtools/SecondOfPairReadFilter.md
@@ -2,7 +2,7 @@
 title: SecondOfPairReadFilter
 summary: Keep only paired reads that are second of pair
 permalink: SecondOfPairReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/SeqIsStoredReadFilter.md b/docs/readtools/SeqIsStoredReadFilter.md
index c95a9208..16bb1c8c 100644
--- a/docs/readtools/SeqIsStoredReadFilter.md
+++ b/docs/readtools/SeqIsStoredReadFilter.md
@@ -2,7 +2,7 @@
 title: SeqIsStoredReadFilter
 summary: Keep only reads with sequenced bases
 permalink: SeqIsStoredReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/StandardizeReads.md b/docs/readtools/StandardizeReads.md
index eb1dfd36..d49be83f 100644
--- a/docs/readtools/StandardizeReads.md
+++ b/docs/readtools/StandardizeReads.md
@@ -2,7 +2,7 @@
 title: StandardizeReads
 summary: Standardizes quality and format for all kind of sources for ReadTools.
 permalink: StandardizeReads.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/TrailingNtrimmer.md b/docs/readtools/TrailingNtrimmer.md
index a9fc7218..4df9f619 100644
--- a/docs/readtools/TrailingNtrimmer.md
+++ b/docs/readtools/TrailingNtrimmer.md
@@ -2,7 +2,7 @@
 title: TrailingNtrimmer
 summary: Trims the end of the read containing unknown bases.
 permalink: TrailingNtrimmer.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/TrimReads.md b/docs/readtools/TrimReads.md
index 93fd4809..d5bb53b7 100644
--- a/docs/readtools/TrimReads.md
+++ b/docs/readtools/TrimReads.md
@@ -2,7 +2,7 @@
 title: TrimReads
 summary: Applies a trimming pipeline to any kind of sources for ReadTools
 permalink: TrimReads.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ValidAlignmentEndReadFilter.md b/docs/readtools/ValidAlignmentEndReadFilter.md
index de1e9607..d5a83f49 100644
--- a/docs/readtools/ValidAlignmentEndReadFilter.md
+++ b/docs/readtools/ValidAlignmentEndReadFilter.md
@@ -2,7 +2,7 @@
 title: ValidAlignmentEndReadFilter
 summary: Keep only reads where the read end is properly aligned
 permalink: ValidAlignmentEndReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/ValidAlignmentStartReadFilter.md b/docs/readtools/ValidAlignmentStartReadFilter.md
index 28f24514..a92c0a17 100644
--- a/docs/readtools/ValidAlignmentStartReadFilter.md
+++ b/docs/readtools/ValidAlignmentStartReadFilter.md
@@ -2,7 +2,7 @@
 title: ValidAlignmentStartReadFilter
 summary: Keep only reads with a valid alignment start
 permalink: ValidAlignmentStartReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---
 
 
diff --git a/docs/readtools/WellformedReadFilter.md b/docs/readtools/WellformedReadFilter.md
index f24575c9..8f8c9573 100644
--- a/docs/readtools/WellformedReadFilter.md
+++ b/docs/readtools/WellformedReadFilter.md
@@ -2,7 +2,7 @@
 title: WellformedReadFilter
 summary: Keep only reads that are well-formed
 permalink: WellformedReadFilter.html
-last_updated: 27-49-2018 03:49:16
+last_updated: 30-57-2018 12:57:55
 ---