From 3a01ec2fb10046d414ebcbfc8e2499f1cbf1336b Mon Sep 17 00:00:00 2001
From: Shubham Chandak <schandak@stanford.edu>
Date: Fri, 3 Jan 2020 16:37:37 +0000
Subject: [PATCH] add support for fasta inputs

---
 README.md            |  51 ++++++-----
 src/main.cpp         |   8 +-
 src/preprocess.cpp   |   4 +-
 src/preprocess.h     |   2 +-
 src/spring.cpp       |   6 +-
 src/spring.h         |   2 +-
 src/util.cpp         |  16 ++--
 src/util.h           |   2 +-
 util/test_1.fasta    | 200 +++++++++++++++++++++++++++++++++++++++++++
 util/test_1.fasta.gz | Bin 0 -> 3949 bytes
 util/test_2.fasta    | 200 +++++++++++++++++++++++++++++++++++++++++++
 util/test_2.fasta.gz | Bin 0 -> 3056 bytes
 util/test_script.sh  |  33 +++++--
 13 files changed, 478 insertions(+), 46 deletions(-)
 create mode 100644 util/test_1.fasta
 create mode 100644 util/test_1.fasta.gz
 create mode 100644 util/test_2.fasta
 create mode 100644 util/test_2.fasta.gz

diff --git a/README.md b/README.md
index 9fa5638..e7c4e2b 100644
--- a/README.md
+++ b/README.md
@@ -72,49 +72,51 @@ Allowed options:
   -c [ --compress ]               compress
   -d [ --decompress ]             decompress
   --decompress-range arg          --decompress-range start end
-                                  (optional) decompress only reads (or read 
-                                  pairs for PE datasets) from start to end 
-                                  (both inclusive) (1 <= start <= end <= 
-                                  num_reads (or num_read_pairs for PE)). If -r 
-                                  was specified during compression, the range 
-                                  of reads does not correspond to the original 
+                                  (optional) decompress only reads (or read
+                                  pairs for PE datasets) from start to end
+                                  (both inclusive) (1 <= start <= end <=
+                                  num_reads (or num_read_pairs for PE)). If -r
+                                  was specified during compression, the range
+                                  of reads does not correspond to the original
                                   order of reads in the FASTQ file.
   -i [ --input-file ] arg         input file name (two files for paired end)
-  -o [ --output-file ] arg        output file name (for paired end 
+  -o [ --output-file ] arg        output file name (for paired end
                                   decompression, if only one file is specified,
                                   two output files will be created by suffixing
                                   .1 and .2.)
-  -w [ --working-dir ] arg (=.)   directory to create temporary files (default 
+  -w [ --working-dir ] arg (=.)   directory to create temporary files (default
                                   current directory)
   -t [ --num-threads ] arg (=8)   number of threads (default 8)
-  -r [ --allow-read-reordering ]  do not retain read order during compression 
+  -r [ --allow-read-reordering ]  do not retain read order during compression
                                   (paired reads still remain paired)
-  --no-quality                    do not retain quality values during 
+  --no-quality                    do not retain quality values during
                                   compression
-  --no-ids                        do not retain read identifiers during 
+  --no-ids                        do not retain read identifiers during
                                   compression
   -q [ --quality-opts ] arg       quality mode: possible modes are
                                   1. -q lossless (default)
-                                  2. -q qvz qv_ratio (QVZ lossy compression, 
-                                  parameter qv_ratio roughly corresponds to 
+                                  2. -q qvz qv_ratio (QVZ lossy compression,
+                                  parameter qv_ratio roughly corresponds to
                                   bits used per quality value)
                                   3. -q ill_bin (Illumina 8-level binning)
-                                  4. -q binary thr high low (binary (2-level) 
-                                  thresholding, quality binned to high if >= 
+                                  4. -q binary thr high low (binary (2-level)
+                                  thresholding, quality binned to high if >=
                                   thr and to low if < thr)
-  -l [ --long ]                   Use for compression of arbitrarily long read 
-                                  lengths. Can also provide better compression 
-                                  for reads with significant number of indels. 
-                                  -r disabled in this mode. For Illumina short 
+  -l [ --long ]                   Use for compression of arbitrarily long read
+                                  lengths. Can also provide better compression
+                                  for reads with significant number of indels.
+                                  -r disabled in this mode. For Illumina short
                                   reads, compression is better without -l flag.
   -g [ --gzipped_fastq ]          enable if compression input is gzipped fastq
                                   or to output gzipped fastq during
                                   decompression
+  --fasta-input                   enable if compression input is fasta file
+                                  (i.e., no qualities)                                
 ```
 Note that the SPRING compressed files are tar archives consisting of the different compressed streams, although we recommend using the `.spring` extension as in the examples shown below.
 
 ### Resource usage
-For the memory and CPU performance for SPRING, please see the paper and the associated supplementary material. Note that SPRING uses some temporary disk space, and can fail if the disk space is not sufficient. Assuming that qualities and ids are not being discarded and SPRING is operating in the short read mode, the additional temporary disk usage is around 10-30% of the original uncompressed file (on the lower end when quality values are from newer Illumina machines and are more compressible) when -r flag is not specified (i.e., default lossless mode). When -r flag is specified, SPRING writes all the quality values and read ids to a temporary file leading to significantly higher temporary disk usage - closer to 70-80% of the original file size. Note that these figures are approximate and include the space needed for the final compressed file. 
+For the memory and CPU performance for SPRING, please see the paper and the associated supplementary material. Note that SPRING uses some temporary disk space, and can fail if the disk space is not sufficient. Assuming that qualities and ids are not being discarded and SPRING is operating in the short read mode, the additional temporary disk usage is around 10-30% of the original uncompressed file (on the lower end when quality values are from newer Illumina machines and are more compressible) when -r flag is not specified (i.e., default lossless mode). When -r flag is specified, SPRING writes all the quality values and read ids to a temporary file leading to significantly higher temporary disk usage - closer to 70-80% of the original file size. Note that these figures are approximate and include the space needed for the final compressed file.
 
 ### Example Usage of SPRING
 This section contains several examples for SPRING compression and decompression with various modes and options. The compressed SPRING file uses the `.spring` extension as a convention.
@@ -183,3 +185,12 @@ Decompressing (paired end) to file_1.fastq and file_2.fastq, only decompress pai
 ```bash
 ./spring -d -i file.spring -o file_1.fastq file_2.fastq --decompress-range 4000000 8000000
 ```
+Compressing file_1.fasta and file_2.fasta (fasta files without qualities) losslessly using default 8 threads (Lossless).
+```bash
+./spring -c -i file_1.fasta file_2.fasta -o file.spring --fasta-input
+```
+
+Compressing (paired end) to file_1.fasta and file_2.fasta (previous example contd.).
+```bash
+./spring -d -i file.spring -o file_1.fasta file_2.fasta
+```
diff --git a/src/main.cpp b/src/main.cpp
index d802037..65acbf4 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -41,7 +41,7 @@ int main(int argc, char** argv) {
   namespace po = boost::program_options;
   bool help_flag = false, compress_flag = false, decompress_flag = false,
        pairing_only_flag = false, no_quality_flag = false, no_ids_flag = false,
-       long_flag = false, gzip_flag = false;
+       long_flag = false, gzip_flag = false, fasta_flag = false;
   std::vector<std::string> infile_vec, outfile_vec, quality_opts;
   std::vector<uint64_t> decompress_range_vec;
   std::string working_dir;
@@ -89,7 +89,9 @@ int main(int argc, char** argv) {
       "reads, compression is better without -l flag.")(
       "gzipped-fastq,g", po::bool_switch(&gzip_flag),
       "enable if compression input is gzipped fastq or to output gzipped fastq "
-      "during decompression");
+      "during decompression")(
+      "fasta-input", po::bool_switch(&fasta_flag),
+      "enable if compression input is fasta file (i.e., no qualities)");
   po::variables_map vm;
   po::store(po::parse_command_line(argc, argv, desc), vm);
   po::notify(vm);
@@ -131,7 +133,7 @@ int main(int argc, char** argv) {
     if (compress_flag)
       spring::compress(temp_dir, infile_vec, outfile_vec, num_thr,
                        pairing_only_flag, no_quality_flag, no_ids_flag,
-                       quality_opts, long_flag, gzip_flag);
+                       quality_opts, long_flag, gzip_flag, fasta_flag);
     else
       spring::decompress(temp_dir, infile_vec, outfile_vec, num_thr,
                          decompress_range_vec, gzip_flag);
diff --git a/src/preprocess.cpp b/src/preprocess.cpp
index e99d42f..cc12e6f 100644
--- a/src/preprocess.cpp
+++ b/src/preprocess.cpp
@@ -33,7 +33,7 @@ namespace spring {
 
 void preprocess(const std::string &infile_1, const std::string &infile_2,
                 const std::string &temp_dir, compression_params &cp,
-                const bool &gzip_flag) {
+                const bool &gzip_flag, const bool &fasta_flag) {
   std::string infile[2] = {infile_1, infile_2};
   std::string outfileclean[2];
   std::string outfileN[2];
@@ -158,7 +158,7 @@ void preprocess(const std::string &infile_1, const std::string &infile_2,
       done[j] = false;
       std::string *id_array = (j == 0) ? id_array_1 : id_array_2;
       uint32_t num_reads_read = read_fastq_block(
-          fin[j], id_array, read_array, quality_array, num_reads_per_step);
+          fin[j], id_array, read_array, quality_array, num_reads_per_step, fasta_flag);
       if (num_reads_read < num_reads_per_step) done[j] = true;
       if (num_reads_read == 0) continue;
       if (num_reads[0] + num_reads[1] + num_reads_read > MAX_NUM_READS) {
diff --git a/src/preprocess.h b/src/preprocess.h
index 49e4287..14f409f 100644
--- a/src/preprocess.h
+++ b/src/preprocess.h
@@ -22,7 +22,7 @@ namespace spring {
 
 void preprocess(const std::string &infile_1, const std::string &infile_2,
                 const std::string &temp_dir, compression_params &cp,
-                const bool &gzip_flag);
+                const bool &gzip_flag, const bool &fasta_flag);
 
 }  // namespace spring
 
diff --git a/src/spring.cpp b/src/spring.cpp
index 419a27e..d75ee99 100644
--- a/src/spring.cpp
+++ b/src/spring.cpp
@@ -44,7 +44,7 @@ void compress(const std::string &temp_dir,
               const bool &pairing_only_flag, const bool &no_quality_flag,
               const bool &no_ids_flag,
               const std::vector<std::string> &quality_opts,
-              const bool &long_flag, const bool &gzip_flag) {
+              const bool &long_flag, const bool &gzip_flag, const bool &fasta_flag) {
   //
   // Ensure that omp parallel regions are executed with the requested
   // #threads.
@@ -60,6 +60,8 @@ void compress(const std::string &temp_dir,
   preserve_order = !pairing_only_flag;
   preserve_id = !no_ids_flag;
   preserve_quality = !no_quality_flag;
+  if (fasta_flag)
+    preserve_quality = false;
   switch (infile_vec.size()) {
     case 0:
       throw std::runtime_error("No input file specified");
@@ -135,7 +137,7 @@ void compress(const std::string &temp_dir,
 
   std::cout << "Preprocessing ...\n";
   auto preprocess_start = std::chrono::steady_clock::now();
-  preprocess(infile_1, infile_2, temp_dir, cp, gzip_flag);
+  preprocess(infile_1, infile_2, temp_dir, cp, gzip_flag, fasta_flag);
   auto preprocess_end = std::chrono::steady_clock::now();
   std::cout << "Preprocessing done!\n";
   std::cout << "Time for this step: "
diff --git a/src/spring.h b/src/spring.h
index 1dc1c86..559310f 100644
--- a/src/spring.h
+++ b/src/spring.h
@@ -26,7 +26,7 @@ void compress(const std::string &temp_dir,
               const bool &pairing_only_flag, const bool &no_quality_flag,
               const bool &no_ids_flag,
               const std::vector<std::string> &quality_opts,
-              const bool &long_flag, const bool &gzip_flag);
+              const bool &long_flag, const bool &gzip_flag, const bool &fasta_flag);
 
 void decompress(const std::string &temp_dir,
                 const std::vector<std::string> &infile_vec,
diff --git a/src/util.cpp b/src/util.cpp
index b44785d..4176e80 100644
--- a/src/util.cpp
+++ b/src/util.cpp
@@ -30,7 +30,7 @@ namespace spring {
 
 uint32_t read_fastq_block(std::istream *fin, std::string *id_array,
                           std::string *read_array, std::string *quality_array,
-                          const uint32_t &num_reads) {
+                          const uint32_t &num_reads, const bool &fasta_flag) {
   uint32_t num_done = 0;
   std::string comment;
   for (; num_done < num_reads; num_done++) {
@@ -38,14 +38,16 @@ uint32_t read_fastq_block(std::istream *fin, std::string *id_array,
     remove_CR_from_end(id_array[num_done]);
     if (!std::getline(*fin, read_array[num_done]))
       throw std::runtime_error(
-          "Invalid FASTQ file. Number of lines not multiple of 4");
+          "Invalid FASTQ(A) file. Number of lines not multiple of 4(2)");
     remove_CR_from_end(read_array[num_done]);
+    if (fasta_flag)
+      continue;
     if (!std::getline(*fin, comment))
       throw std::runtime_error(
-          "Invalid FASTQ file. Number of lines not multiple of 4");
+          "Invalid FASTQ(A) file. Number of lines not multiple of 4(2)");
     if (!std::getline(*fin, quality_array[num_done]))
       throw std::runtime_error(
-          "Invalid FASTQ file. Number of lines not multiple of 4");
+          "Invalid FASTQ(A) file. Number of lines not multiple of 4(2)");
     remove_CR_from_end(quality_array[num_done]);
   }
   return num_done;
@@ -276,14 +278,14 @@ void write_dna_in_bits(const std::string &read, std::ofstream &fout) {
   for (int i = 0; i < readlen / 4; i++) {
     bitarray[pos_in_bitarray] = 0;
     for (int j = 0; j < 4; j++)
-      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[4 * i + j]]<<(2*j)); 
+      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[4 * i + j]]<<(2*j));
     pos_in_bitarray++;
   }
   if (readlen % 4 != 0) {
     int i = readlen / 4;
     bitarray[pos_in_bitarray] = 0;
     for (int j = 0; j < readlen % 4; j++)
-      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[4 * i + j]]<<(2*j)); 
+      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[4 * i + j]]<<(2*j));
     pos_in_bitarray++;
   }
   fout.write((char *)&bitarray[0], pos_in_bitarray);
@@ -330,7 +332,7 @@ void write_dnaN_in_bits(const std::string &read, std::ofstream &fout) {
   for (int i = 0; i < readlen / 2; i++) {
     bitarray[pos_in_bitarray] = 0;
     for (int j = 0; j < 2; j++)
-      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[2 * i + j]]<<(4*j)); 
+      bitarray[pos_in_bitarray] |= (dna2int[(uint8_t)read[2 * i + j]]<<(4*j));
     pos_in_bitarray++;
   }
   if (readlen % 2 != 0) {
diff --git a/src/util.h b/src/util.h
index 256685e..72109cf 100644
--- a/src/util.h
+++ b/src/util.h
@@ -52,7 +52,7 @@ struct compression_params {
 
 uint32_t read_fastq_block(std::istream *fin, std::string *id_array,
                           std::string *read_array, std::string *quality_array,
-                          const uint32_t &num_reads);
+                          const uint32_t &num_reads, const bool &fasta_flag);
 
 void write_fastq_block(std::ofstream &fout, std::string *id_array,
                        std::string *read_array, std::string *quality_array,
diff --git a/util/test_1.fasta b/util/test_1.fasta
new file mode 100644
index 0000000..4650531
--- /dev/null
+++ b/util/test_1.fasta
@@ -0,0 +1,200 @@
+@SRR554369.1 1/1
+TAACGAAACCGGCATGGAACCTCCTGTTNTTGTGGCGGGGGGGGGTAGGCTAGAGAGCTGGCGCCCGCAACCCGGGGGGGGACTTTNNNGGGGGGGGCGG
+@SRR554369.2 2/1
+GATGACCCGCCACTTGATCAGCGAGTTTNCACAGTCGAGCTCAAGAATCATTGACGCAACCTCAAACTAAGCTCCCCTCCACTGAANNNCTGCTCCACGC
+@SRR554369.3 3/1
+ATTCCAGAGCTGCCTTCTGAAGCCGACTNTGAGACAAGCCCTGAATCTGAAATAAAGGAGGAAACCGATGCAGATCGACATTGATANNNGTAAGGTCGTG
+@SRR554369.4 4/1
+GGATTCGCAAGAAAGGCTTCGCCACCAANTCTGCCGCGATTCGCTATGAGCAGGATTTTTCGCCGTGAAGGGCGAGACGGGCCGANNNCTGGATGACCG
+@SRR554369.5 5/1
+GCCACAAGAACTAGTCGATGACTTTGAGNCCCGAAGAGTCATTCTTTTTATCGGATCTGGCGTCTCAAGAAACTCCGTGGGAGCAGNNNNGAGAACTAGA
+@SRR554369.6 6/1
+GATCCGCCGCAAGCCCTACTCGGTGGTGNTGCTGGACGAGGTGGAGAAGGCCCATCCGGATGTATTCAACATTCTCCTCCAGGTGCNNNAGGACGGACGC
+@SRR554369.7 7/1
+GATGTGCGGGCTTTCATCTGACGCAATTNGGGGATTCCTGTCAATGCTGGCAATGGAATAAGGCAAGGATCTTTGAACCCTATGGANNNCGCTAGAAACA
+@SRR554369.8 8/1
+AAGTGCGTGGCGCACTGGGCAGCCAGACNTTGATCATGTGGTCGGTCAACAGCGTGCCCGGCATCTGGGTTTCCTTTGATATCAATNNNGATCAGTATTG
+@SRR554369.9 9/1
+TACTCAACCACTTCTATTGCTCCTACGCNAAGCCGATCATCTTCTATCGTCCGCCCAAGCTGAAGGCAGTCGACGAATTGCTGAAGNNNCAACGCGTGCA
+@SRR554369.10 10/1
+TTCACGACGTTCGCCCGATTGCGGACGGNCGTCGCGGTCACGGTTGAATGCGGGACGCTCACGGCGCTCACGGGAGAATTCACGAGNNNCACCCAGTCGG
+@SRR554369.11 11/1
+AATCAAACAGAACGGCGGCGTAACGCGTNATAACTACTTCTCCAAACGCTCAAGAACGGCCTGACAGGCAGCCGGCAAGGCGGCCTNNNGAACCAGAGGC
+@SRR554369.12 12/1
+CGGCCGCTCCACCGCCAATGCCCTGTGGNGCAACGCGCCGAGCGTGCTGGTAGGCGACTTCCTTTATGCCCGCTCCTTCGAAATGTNNNTCGAGCTGGGT
+@SRR554369.13 13/1
+CAGATCCTGCATGCCCTCGCCCACGCCANTCCAGTAAACCGGAATAGGACGTACGCCTTGCGCACAGGCAGCAACGGCAGCCACAGNNCCGCCTTTGGCC
+@SRR554369.14 14/1
+GTTTCGGGTCTATACCCAGCGACTAAACNCCCTATTAAGACTCGCTTTCGCTACGCCTACCCTATACGGTTAAGCTTGCCACTGAANNTAAGTCGCTGAC
+@SRR554369.15 15/1
+GCGTACGGTCAGGCCCGCTTCTTCGAACNGTTTCAGCAGCCACTGACGCGATTGCAGAAACAGATCGGAGAATGCACGGCGTGTCCNNGGCTGGTCGGGC
+@SRR554369.16 16/1
+TTCGGGATATGCCTGTAACCCGCGCGCTNTCTGGCGCCAGGTTTTTCCATGGCGCTCGACGAAGCAATCCGGGTTTCACTTTTGCANNGAACTGATTCAG
+@SRR554369.17 17/1
+ATATCAAATCCTTTCTGTCCTGCCCGGCNCGTAGTGTCCAAGGCGAAAAATGAACATGCTGCTTTTTAACGACCACCTTGGTGCAANNTTTAGACCTGTA
+@SRR554369.18 18/1
+TGCACGTTCTTTTCTTCTTGCATCATGTNGTTGATGCGGTGGCCAATACCCTTGGCAGCCCAACCCAGGTGAACTTCCAGAACCTGNNCCACGTTCATAC
+@SRR554369.19 19/1
+AATGACCCTACCTTGCTGTTCACTAACGCAGGGATGGTGCAGTTCAAAGATGTGTTCACGGGCAAGGAAACCCGTCCCTACAACCGNNCAACCAGCTCTC
+@SRR554369.20 20/1
+CATATGAGTGAACACACCGTTTCCAAAGACGCCACCATCTCCTTTCGTCGCATCAACGCGAAAACCGTCTACGAGGTATGTGAGCTNNGCGAGACCCTCT
+@SRR554369.21 21/1
+GCGTAAGCCCTAGGAGGCCGCGATGCTCCGTTATCTCTCGTTGTTCGCGGTAGGTCTGGCCACCGGCTACGCCTGGGGGTGGGACGNNCGTCCTGCTGCC
+@SRR554369.22 22/1
+ATTGCAAGCAGGGCACAAACGGGCAGAANGGCGAGTGCATGACTCACGAGCTTTGGGCGACGCTTAGTCGTAAAATGGTCGATTATNNGGATTCTGTCTC
+@SRR554369.23 23/1
+ACCGGGTTGCCCACAGTTACTGCACTAGNCAAGGCACCGGGGAAGCCGGTCAACCATTTTGGCCAGGTAGCGATTNNCCGTACCGGCCA
+@SRR554369.24 24/1
+GTCTGCCCGGTCGAGTTTGCGCGTGAAACGCTGGAGCTTTATACGCCCTTGGCGAATCGTTTGGGGATTTGGCAGATCAAGTGGGANNTGGAAGATCTGG
+@SRR554369.25 25/1
+CCAGCAACACCAGACCACCAACCTGCAGNACGAGTCCGTATATGGCGGCTCCAGCTTGCTACTGGGTCGCGGGGGGGGTTCGCCGGNNGTGCCGGCCCCG
+@SRR554369.26 26/1
+CCAGCAATACCTTCTACGCGGGCATAGANCATCGCTTTTCCAATGGCTGGTCCTTGAAAGCCAATGTCAGCCGTCTGGAGAGCGAGNNCGACTCCAAGCT
+@SRR554369.27 27/1
+ATAACATAAAGCGGAGTTTGAAGTATTANTTAAAATGTCACTATTTTCATCAGCATGAGCTGAACAACATAGCGTCAAAAAAAGACNNTAATATAGTATC
+@SRR554369.28 28/1
+CAAGCCCTTGATTCTGTATTACGACTCCNTGATGGGTATGGGCTCGGATGCCACGGTGGACTGGATGCGCCGTCAGCTGGCCCAGGNNGGCTTGCAGCTG
+@SRR554369.29 29/1
+AGCGCGGTCAGCACGATGGGCCGGAAAGGCCGCACGGCAGCCTCGATGATGGCGTGCCAGCGATCCAGTCCATGGCTGATGTCCTGNNCGATCTGGTCCA
+@SRR554369.30 30/1
+AGGCGCCCCCTGACCAGCTCGGCCTGCCGAATCTCGCCGTCGCGCCGGAGCGTCCAGCGGCGATAGGCCAGCAGGTTGTCCAACGGNNCGGTCAAGGAAC
+@SRR554369.31 31/1
+TGGGGGGCGGAAGCGGCCAGCCGTGAACAACAACAAACAACGCTGCGACTGTCCGGCTTTTTCGCCGACCGGCTGCGCGGCATTTTNNCCCTGAGCCTGG
+@SRR554369.32 32/1
+GGTTCGTCGAAGTAAACAACCTTCACGACACGCAGGTAGTAGAAAGCACCAATCAAGGACATGATCACGGCAAACACAGCCAGCCANNCATAGCCTGCAC
+@SRR554369.33 33/1
+CACCATCTGGAAGCTCTTTCTTTTTGCCGGCTTCTTCATCCAGGGTGACAAAGGCACCCCGGAAAAAAGTGGTGGCAGCCAAAGATNNCTGCCACTCGTC
+@SRR554369.34 34/1
+ATCTCCTGAACCTTGTTCTCGCCCATTCGCGACAGGCCCAAATCCAGGGCTTGAGCCAGCACGGGCACAGGAAAGGTTTTGCTTACNNGTAAAAGAGCCA
+@SRR554369.35 35/1
+TTTCATTCCGGTGACGCGGAACTTTCAGCCGCCATGCATTCTGCAACTAGTGGCCATTGGCAGGCATTTAACGGAAAGGCCATCAANNTGGTATCAAGTG
+@SRR554369.36 36/1
+ATGCGGTTTCTCCAAACGAATCGGCGGGCAATCCTGGCGCACGTCGCTTGTAGCACATCGAACCCGTTGGCGAGAGGGGGTGTGCGNNGCTAGTATGGGC
+@SRR554369.37 37/1
+AAGTTCAGGAGCAAGGCTGGGTGGTTCCTTCCTTCGAAGTTCGTCGCGAGCAGATTCGCACCGACCTGGAAGCTGAAGCCCAACGCNNGAACTCCACCTT
+@SRR554369.38 38/1
+AAGCTCAAAGATGTCTGCTTGCTGGCAACGGGCGACCTGCTGTGCAGTGATGGGCGACTGACTTCCCACCAGAATCAGCACCGGCTNNGTACTGGCGTGT
+@SRR554369.39 39/1
+CCAGGCTGTAAAGGCTGGCAACATCCTGGTTCGTCAGCGCGGCACCAAATTCCACGCCGGTTACGGCGTTGGCCTGGGCAAGGACCNNACCCTGTTCGCG
+@SRR554369.40 40/1
+GCAAAGCGTTTATTTTTGCAAAAGTTGGTAAACGAAAATTAAACGGATCGGATACATTATCCCAATCATTGCTTAACTCTTGATACNNGCCCGAGCCCAT
+@SRR554369.41 41/1
+AACCTCGCCTGAGTACACCCAGCAAGGTTACGACAACACCTTCCGCATGATGACCAGCGACACCCAGCAAGGTGCCGCTGTGGGTCNNTTCATCGTCAAG
+@SRR554369.42 42/1
+GGTCAGCGCCTTGACGATGAAATCGCCGCTGGGCAGTGGCTTGATGTAGCTGTCCTCCTCGACGTCGTGCTCGTCCTCGATATCACNNACGATCTGTTCC
+@SRR554369.43 43/1
+GATGAATGCGGCGGCACGTTTTGAGGAGGTCGAGGCATAAGCAGCCATCAAGCTGCGGTGGGCCGCGCTAGCTTCTGTGTGTAATANNACGGCGCGGGCC
+@SRR554369.44 44/1
+GTCACCGTCGTTGAACTGCACGCCGATGCCCGCCGCACGGTTGCCCTGAGCGCCCTTCGGGGCGATCCAGACGACCTTGCCGTCCANNGGGATCTTCTCC
+@SRR554369.45 45/1
+AGGTCGGCATGCGCCAGCAAGGGAGCAGCCAGAACAGCAGTTGCAAGGAACAGGTGCTTTTTCATTGTTATTTCTCCAGTGTTCAGNNGTGGTTTGCCCC
+@SRR554369.46 46/1
+CATTGACGCCCTTTTGCTGCTCTGCGTGCGAGACCAAGGCCCGATATGTCGCTTCCAGTTTCATAGTTCGACATCAGATGATTTGACNTCGAACCTTAAT
+@SRR554369.47 47/1
+GCTTGCTCCGCAGCCTTGATGGCCTCGTCATAGCCTTCACGTAATTTGGCAAAGACAGGGCCGGGTCGTCCGTCGCCGACGGGCTGNNCGTGAAATACAA
+@SRR554369.48 48/1
+GGCTACATCATCGGCCTGGCCGAAGTCAGCTTCATCGCCTCGCAGATCAATACCCAGGTGTTCACCCTGCCGACCCAGGTCTACCTGNTCCTCGGCCTCC
+@SRR554369.49 49/1
+TGGAGATCAGGTCGATCTTGCTGACCAGGATCACGTCGGCGAATTCGACCTGGTCGATCAGCAGGTCGGTGATCGAGCGCTGATCCTNCTCACCGAGGGT
+@SRR554369.50 50/1
+GGGCAAGACCATGACGATTTGCGGGAATATCGTCACAATCACCGTGGCCAGAACCAGCACCAGGAAGAAGGGGAAGGCCATGCGCANNAGCTCGAACAAG
+@SRR554369.51 51/1
+TACCGCTAACGTGGCCAATGCAGCTGGTCTGCCCAAGCCAGATGCCGCCAAAGGCGAGCCGCTCTACCTGCAAGGTGCGATGTCGCGNGGCGTGCTGGCC
+@SRR554369.52 52/1
+AAGAGGAAGGCGGGAATGGCGTAGCCGACGATGATCGCCGAGCTGGTCCAGATGTCGAAGACGCTACCATGGCGGACCGCCTTGGCNNTCCCCAGCGGGA
+@SRR554369.53 53/1
+ACCTGGCGGCGATCACCCACGGTTTCCGCGAGCCGCCGCCGGAGATGCGTTTCGAGGAGGGCTGAGACAGAATCGACGCCCGTTTCGNGGCGGCGAGGCG
+@SRR554369.54 54/1
+TGCTGACATCCTGCTGGGAGGGAATCTCGTACATGGTA
+@SRR554369.55 55/1
+CAACGGTTCGCTGAGAATTAGAGGTATGCCGAGGGACTGGAAGATGCTTGGCTCTTCCTTGGTTTCATGCTTCTCTTGAAGAGTTTCNCATGGAGCTCGC
+@SRR554369.56 56/1
+CATATCGGCCTCGGCAGCGGTCTCGACGATGCCGTCTTCCAGGCAACGCACGGTTTCCAGGCACAGCGGGATCATCATGAAGTTGACNATGTCCTCGTCG
+@SRR554369.57 57/1
+ATACACGCTTGCATTGGATCATCGATCGACTCCCTGGTTGCGATGAAGTCCGATCCGGACTTGAGCTAGGCCCGGACGCTCGGTAACNTGGGCGCATTTT
+@SRR554369.58 58/1
+TCTCATTCATTCCATCGCCAGCCGATGAACGGTCGTCTCCGGCCGAATCGCAGGCAAAAAAAGACCCGGCAAAGTGCCGGGGCAAAANCCGTGATACGCC
+@SRR554369.59 59/1
+CATGCTGATCTGGCGGCTGCGCATGTCCTCCGGCGAGTACTCCTCGTCCGGGTATTCCTCGCGGTTGAAGCTGCGCAGGCGACTGCCGCCGCCGGGCGGC
+@SRR554369.60 60/1
+GGACATGGGCCTGCCCGAAGAAAATGTCTGGGTCACCGACATTGACGGCGTGGTTTACAAAGGCCGCCCTGGTCACCAGGTTCCTGANCTGGCCCGTTTC
+@SRR554369.61 61/1
+TAGAGGTCCTCCGCCTTCACCCCGTCGGCCAGCAACGCCACTTCCAGGGTGTACTTGGCGCCCTTGCGCAGGCCACGCTTGCCGGGGAACTCGCGGACGT
+@SRR554369.62 62/1
+CATTCACGGCGGTCTGCAAGAGGGGATGCAAATCCATGACGCCGCTGATGATGCTGGCGCTGTGGATCAGACGTTGTTCACGTAGGGNATCGGCCGCCAG
+@SRR554369.63 63/1
+GTGACAATATCGGCCACCCGGTCAAACGCGGCATTATCGAGCAACAAGCCACCGAGCACCGACTGCTCCGCCTCAATGGACTGAGGCNGGAACCGGCGGG
+@SRR554369.64 64/1
+AAACTTCATAATTCTTTCTGGACGGCGGGGGCCTAACAGGAAGACTCGTCCCCAACGGCACGATGTGCCTGCCCCCATGACAGCGGCNAAATACGCCGCC
+@SRR554369.65 65/1
+AAACGGCGTCCTGCAGGAAGTGCATGTCGAACGCACCCAGCGGCGCGGCATCGTCGGCAATATCTACAAGGGGCGGGTGGTACGGGTACTGCCGGGGATG
+@SRR554369.66 66/1
+CCGTGCTGGTCCTGCGCTTCGAAGCGGACACCGAGGAAGAGCTGGAGCGCATCAAGACCGTCTTCCGTAACCAACTGAAGGCAGTGGATTCCTCGCTGCC
+@SRR554369.67 67/1
+GTCGTCACGCCGGCAACGACCCCTTTCGGCGAAAGCTTCGCCAGGCCTCCCCTGGGGGCCAACGGGACATAACAGTCAACAAGTGAGNGCAACACCCTAT
+@SRR554369.68 68/1
+AACCGCGCCTTTGGCTCTCGCTATTCCACACTGCAACGCCAATACAGCTGGCAAAACGATCTGACCGTGGCGAAGGGCCATACCGTCTCCTTGCTGGCCG
+@SRR554369.69 69/1
+AACCCACAGTGGATTGCTTGATACCCATACGCTCGAGCTTGCGCATCACTTGGGGCAAGACCGCATCAGACGACGCTGTGCCCAGCACAACCAGCAATTC
+@SRR554369.70 70/1
+AAGGGCTGATAATCAGCACGAGGTTGAACAAACTGCGTTGCACCTCGAAGCCAGCGATGTGGATACGATAGACGGGGCGCGACGCTTTAGCGGTTTATAG
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+CCGCAGTGACAGAAGGAACAAAGCCGTCCCGATCACCAGCAGGGCTAAAAAGGGTTGCCATACGGTTTCAATGCCAGCCCCCCGGCACAAGATGGCCTGC
+
+AGCACATACGCCCCCACCGCATGTGCGCAGCGAGCAATCGCAGGAATATCCTGAATCTCGAAAGTGGCCGAACCGGGCGACTCTACGTACACCACCTTGG
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+
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+AGGTCGTCAGGCCTTCCAGGCCGACCGGGCCACGGGCATGAAGACGGTTGGTGGAAATGCCGATTTCGGCACCCAGGCCGTACTCGAAGCCGTCGGCAAA
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+TATGCCGTCGCCGTTGGCGTCGATAATCCATTGGAAGGTTTGCATGACAATTCCTTTTATCAAGTCCAGCAAGCTGCGCCGGAATTACAAGGACTGCCTT
+@SRR554369.76 76/1
+GCTGACCGAGCCTAATTGTGCAATGCGTAAAAAACAGCGCAAGGAGCGATCCAGATGATCGGTGGGGCGGGAATCGTGCATGCCATTGTCTCTTTATTGT
+@SRR554369.77 77/1
+CGGGACGAACGGTGTTTCATACCCGTCTTTCTTTCCCAGGCACAACCAGTCCTTACCCTGCCCTGAGGCCACAAGCTTGTTGATTCAACAAGTCTTTCGT
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+CTGATTCCAACGCTCCTGCATATCCTCTGGCATCGTACCAGGCCCCAAGAATGCATACCAATTTAGTGCAATAAAACCAGGGTAGCCGGCCTCTGCCACT
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+TTTGTGGTGAGTGTAATTAAATAAGGCGAATTTGTTTGGAATGGGTCAATTTGAGTTAATGTAAGCATTTGAAGCGAATGTATAAAATAAAAACGTATCG
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+ATGCCGCCAACAAAACGCCCAGCAGCAACCACCAGATGATGCGCAAGGTGTCGTAATCGAGAAGAATCAAATTTTCCATGATGGTTCCCCCTCCTTAACC
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+TTTCACGCCCAGGACTCATCGCGCTTTATGCGCTGATCCCTTGCCTGGCCTTGACCTTTTCACATCTGGATTCTTGCCTCATGTCCCGTAACTCCGAACT
+@SRR554369.82 82/1
+GCAAACCGGTTAAAGCCAGAATCGCCCAGGCAGGCACCTGCTGCAAGACACGCTCCACCGGCAAAATGGCATGTGTCAGAATCCAGGCGCTGATCTGGCG
+@SRR554369.83 83/1
+CGGTCTCGGTGGCCACCACCTTCCGCAAAGAGCTGGAAGAAGTGGGCGTGATCTTCTGTTCCTTTTCCGAGGCCGTGCGTGAATATCCGGAACTGGTGAA
+@SRR554369.84 84/1
+GATCATTGAACGATGCTCCGAGCACAGGGCCATTTCGGCCCAGCGTCACTCGTGTCAAATTGACAGCAAATCCGACACTACGTCTTAAAAAAGCTGTAAT
+@SRR554369.85 85/1
+TGATACATCGCTGCGCAGTGGCGACAACCTGCAAGCGGCAGAACAGTTGTCGCAGGTTCTGAGCAGCCTGCAATACATGAGCGATGTGCAGTTGCGCCGT
+@SRR554369.86 86/1
+TCTGATGGCAGGCGTGGGCGTAGTCGTGATTGCCACTGTGTTCAATACCGTCCGTCTGCAAGCCCTGAACCAGCGTGAAGAAATTGCCGGGGCCCGTCGG
+@SRR554369.87 87/1
+TGGTGCACTGACAGGCGCGATGGCCCGGCGGGCCTGCTAGATCAGCAGTTCCGCCCTGCCGGCTGCGACCTTCAGAATCTCCGCGCCGGTGCATCCACGT
+@SRR554369.88 88/1
+TGAGCAGCCTGACTCGCTTTGGCTGCTGCATTGGTGGATCACGACGCATGCCGACGTTGCCGTTTGGAGCCTTGTTTTCGGCAAGAGCACCTACTCGCGC
+@SRR554369.89 89/1
+GGAGATCAGGGCGGGGCCTTTGTAAATCAAGCCGGTATATAGCTGTACTGCTTGGGCTCCGGCCTGGATCTTTTCCTGAGCCTGACGGCCAGATTCAATA
+@SRR554369.90 90/1
+GAAGCCAGATCGGGATACAGCTCGATCAGTTCGGGCAGCAGTGCATCTTCGCTGAGCGGGATGATGAAAATCGTCTTGCCATCTACGCTGGCCAATGTGG
+@SRR554369.91 91/1
+CCTGCGCCAGGCCCTGGAGCGCCGGCAACTGGTCTTGCACTACCAGCCCAAGGTACTGGCGCCGAACGGACCGATGATCGGCGAGGAAGCGCTGCTGCGC
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+AGTAGAACAGGATAGGCTCGCCGCGCCGATAGCTCGACAGCACCGCCGCGTCCAGTGCCGGGCCGGGGCCCGGACGGAAATTGGGGAACGTCTCCTCCAG
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+@SRR554369.94 94/1
+GTGAAGTGCGCGCGCATGCGCTCGCTCATGTACTCCTCGCCCTTGGTTTCCTGATAGGGTTCGAAGCCGCGGGTCATCTGCTGGCTGCTCTGTTGTTTTG
+@SRR554369.95 95/1
+GTCCACGCCGTAAACGATGTCGACTAGCCGTTGGGATCCTTGAGATCTTAGTGGCGCAGCTAACGCGATAAGTCGACCGCCTGGGGAGTACGGCCGCAAG
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diff --git a/util/test_1.fasta.gz b/util/test_1.fasta.gz
new file mode 100644
index 0000000000000000000000000000000000000000..ace56debbbef8d7fb135836695a266f755609a32
GIT binary patch
literal 3949
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Huq^-p*u3KM

literal 0
HcmV?d00001

diff --git a/util/test_2.fasta b/util/test_2.fasta
new file mode 100644
index 0000000..8ce176a
--- /dev/null
+++ b/util/test_2.fasta
@@ -0,0 +1,200 @@
+@SRR554369.1 1/2
+GTAGAAGAAGANAGCACACTGGCCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.2 2/2
+CGATAGTCGAGNAGCGCTGCGCCTCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.3 3/2
+TCCTTGATAGCNGCCNNNCAAGCTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.4 4/2
+
+@SRR554369.5 5/2
+ATGCGGNTANGNNGNNNNNNCTAGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.6 6/2
+GCCAGCTCCTGGATCTGTGCCGAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.7 7/2
+CTATTTCCTCCGAATAATCTCTTCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.8 8/2
+AGGCCGGTTCACAAAACGCACACTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.9 9/2
+CTTGCTGATCAATGCAGTGGTGCCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.10 10/2
+GTGAGCGTCCCGCATTCAACCGGGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.11 11/2
+GATGCCATTCGCGATCAATTCGCCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.12 12/2
+GTCTCTTCGGTAGTGCTGGCGTCGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.13 13/2
+AGCTCAAGAAGATCAAGCGCGTCATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.14 14/2
+AGAGGGGAGTGAAATAGAACCTGAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.15 15/2
+GGCCATGCCCTTGTTGAATCAGGAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.16 16/2
+GACCTGGGAAAGGGGAGGACGCATGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.17 17/2
+CTCAAGAAGCGGCGCAACGCATTCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.18 18/2
+AAGCGTCGTCTGCAGCCTGGTGACAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.19 19/2
+GGTGGCGGGCGGTGTAGCCCACGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.20 20/2
+GTAGATGGCACGGAACCAGGCATTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.21 21/2
+GCAGAGTCAAATAGCCCTCTGCCTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.22 22/2
+GGCTTCCTGAGCGGCCAACTTGAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.23 23/2
+TGCCTGCAGGAAGCCAAGCCGGATGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.24 24/2
+CGTTTCAAGGCTGCCAGCAGTTGGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.25 25/2
+GCTGCCTTGTAGTGGCCACGCGCATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.26 26/2
+TTCTGATCGAACTCCTGATGCGAGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.27 27/2
+CGGGATAGCGATCACACAGGAAGTGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.28 28/2
+ATACAGCAAGGTGAAGAAGTTTTCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.29 29/2
+GGACCATCGCCCTGGCCGGCATGATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.30 30/2
+AGCCGTCTGAGCGCGTTGCTCAGCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.31 31/2
+ATGGTACGTGTGCGCAGCTCCTGACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.32 32/2
+GTCTGGCTTTGATCTGGCTGCTGTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.33 33/2
+GAGGGTTCGCATGGGGCCGCTGGAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.34 34/2
+GCATTGATGGCTTCTTCTGACTCTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.35 35/2
+AATATTTGGAAATATCCGTTTGATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.36 36/2
+TGGCCGACATGACGTGCCTCCAGGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.37 37/2
+AACAGCGGGAAATACTTTTGATTCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.38 38/2
+ACAAGCTTATTTAAGCCAACGGCCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+@SRR554369.39 39/2
+AAAGCCCCGTCGCGAGACAGGGCTTTNNNNNNNNNNNNNNNNNNNNNNNGNNNCGANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNCTTG
+@SRR554369.40 40/2
+GGCTTGCCCTGGGCCAAGGCCAACATNNNNNNNNNNNNNNNNNNNNNATCGTAGTTAANNNNNNNNNNNNGGCATTGTCCTNNNNNNNNNNGTCGGTAGG
+@SRR554369.41 41/2
+TGATGTTGGTCAGAATGGAGGTGAAGNNNNNNNNNNNNNNNNNNNNNNNTNCACGGGNNNNNNNNNNNNNNNNNNCNTNNNNNNNNNNNNNNNNNNCCTG
+@SRR554369.42 42/2
+CAACGTGCTGCTCCGCGAATTCCGCGNNNNNNNNNNNNNNNNNNNNNNNGNCATCGANNNNNNNNNNNNNNNNNCCGGCNNNNNNNNNNNNNNNGGCGAC
+@SRR554369.43 43/2
+GGACGTGAATGCAGTTTTATCCGCTCNNNNNNNNNNNNNNNNNNNNNNCAGAGTCGCNNNNNNNNNNNNNGCCACTTACCNNNNNNNNNNNNCNCGCGCC
+@SRR554369.44 44/2
+ACTACAAGCTTGGCGACGAGGTCTTCN
+@SRR554369.45 45/2
+CTGCCGGGGACAGGATGCAAACGGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNCNGN
+@SRR554369.46 46/2
+CAATGCCGAATTTGGGCGCCACTCTTNNNNNNGTAGGCNNNTNACTACCTGGAAATATTNNGCNTNTTGGATTGGATTGGCANGANGNNAAAGCATCACC
+@SRR554369.47 47/2
+CGTCAGCCACCAAAGAGGTGCTGCCCNNNNNNNNANNNNNNNNNNNGCCCGTCGGCGANNNNNNNNNNNGCCCTGTCTTTGNNNNNNNNNNTGCAGGCTA
+
+GTACCATTTGTTGACCTTTTCCAGCCNNNNNNTCGGGCNTNCTTGGGATTGCCACGCTGCGCCNGGCGGCGTTCGAGCCAGAAGGCGAAACGCGACAGTC
+@SRR554369.49 49/2
+TGAATTTTCTCCGCGACTACCAGGAGNNNNNNNNCCNGNNNNNNNGTGGCGAAACCCTCNNNNNNNNGGATCAGCGCTCGATNACNNNNNNGCTGATCGC
+@SRR554369.50 50/2
+CTTGACAGTGGAGACGGCGCAGATCANNNNNNNNNNNNNNNNNNNNNTGTTCGTGATTNNNNNNNNNNNNGGGCGCAACTTNNNNNNNNNNGTGCGCATG
+@SRR554369.51 51/2
+GTTGACCGGAATAATGCTGTTGCCGCNNNNNNCGTGACNNNTNANACAGGCCAGCACGCNNNNNNNNCTCTCACCCTGCAGGNACNGNNNCCCGCCTTCG
+@SRR554369.52 52/2
+TGATCATCGAGAAATTGCCGGTGTCGNNNNNNNNNNNNNNNNNNNNNNCGCTGATCATNNNNNNNNNNNNGATCCCGCTGNNNNNNNNNNNGGNGGTCCG
+@SRR554369.53 53/2
+CATCGGGAAGGGGAAGGAACAACGCTNNNNNNGACATGNCCGGCTCCGGAATCAGGGAGGCGATGGATAGCCACTCTAGGCCAGGAGCCTGCGCCTTGCG
+@SRR554369.54 54/2
+CGAGCCGAAGAACGCTCTCACCAAGCNNNNNNCCAAGCTGTTCGAAATGGAAGGCGTCGATCTCGAATTCCGTCCGGACGCACTCAAGGCGGTTGCCCGC
+@SRR554369.55 55/2
+AGGAAAGGTATAAAAATTCTCGACGGNNNNNNAGAAAANNNANACCCATACAAAAAGAGNCATNNNTGCAAAAGCCAGAGCCNGGNCNNGCAGAGCGAGC
+@SRR554369.56 56/2
+CCGACAAGCGCGGCAAGCCGAAGAAGNNNNNNGATCCGCAGGCCTACGAAGTGCTCAAGCCGATCGTGGTCGAGCAGCGCGAAGAGACCGACGAGGAAAC
+@SRR554369.57 57/2
+ACACTGGTGCTCGGCGATTCGGGCTTNNNNNNCTGGCANGNGGCGAACAAGGGGAGCAGGCTGNAGACCAGCAGACGGGCAGGGCGCCTAGGGAAGACTC
+@SRR554369.58 58/2
+AAAGCGTTTGACATGGAAATGAGAATCNNNNNTATGTCACTCAACTGGTCGCGAGATCAGCCGGTAAGCTGAGAGACCCACGCAGTCGGACTCTTCAGAT
+@SRR554369.59 59/2
+GATGGCGAGATCTACGCCCTCGAACATNNNNGCATGCGGCGGGAGAAGTTCGTCTATCGCCGGCCCGTCGGCGGCATTCCGCGTCCGGGCTTCGACCGCG
+@SRR554369.60 60/2
+ATCACGAAGGGACGGTCTGCCATTTTCNNNNGCATTTCAGCTTTCAGTACGCCACCGGCGGACAGGCCTACGAACACGTCAGCATTTTCGATGACATCAG
+@SRR554369.61 61/2
+GGGGTGGCCACCTACGTCTGGTCGATGNNNNTGGCCTACGACTCGACGAAGCTGGCCAGGGCGCCGCAGTCCTGGGCGGATTGCTGGAACGTCCGCGCGT
+@SRR554369.62 62/2
+GTCCACGCGCACGCGACGCAATTTAATNNNNNCCCGCAGCGTATTCATATTAGTGGCAGCTCGGCAGGGGGCCATTTAAGCGGGATGTTGGTGGCGGGCG
+@SRR554369.63 63/2
+TCGGTCCTGTCAGCCCAGCACGCTGTTNNNNCTGACTGCTCTGACCCCAGATACACATACTGTTCAAGCCCGCACAACACATGCTGTTGGCTGCGGCGTC
+@SRR554369.64 64/2
+GTCACACCATAACGGCGTTCGGGCTCCNNNNNCCCTAGCGCAAGCTTTCTCTTTTCTGGGTGAAGTTTTTATGACAAAGGCGGCGTATTTTGCCGCTGTC
+@SRR554369.65 65/2
+GGATGAACGCCGCACGTTCCAGGCCGANNNNGACGAACGCCGCCTGCATCCCCGGCAGTACCCGTACCACCCGCCCCTTGTAGATATTGCCGACGATGCC
+@SRR554369.66 66/2
+CTCCTCGCTCTCCATGGCGTTGCCGCCNNNNTTGATCACCAGCGTCTTGCCGACGAAGCGGCGGATGTAGGGCAGGGCCTCGGAAAGGCCCTGGGAAACC
+@SRR554369.67 67/2
+ACAAAGATCACGAGATTTACCGGTTATNNNNNTCTGATAACCACGCAAGAAGGCTCTTTCCAACGGATCACGCTTAAGTCTTCTCATAGGGTGTTGCCCT
+@SRR554369.68 68/2
+ATATTGTCGTTACGCACGCTGGCTTGCNNNNGGCGTTGATTGATATCGCCACGGGAAATCGGGGCAGAGGCATTGGGGTTGCGCGTGTGGACCTTGTGGA
+@SRR554369.69 69/2
+GGGCGTCTTGGGGCTGATCTTGCGCATNNNNGGCTTTAGCATCATCAAGCTGTTGAAGTATCTGCGCGAGGAATTGCTGGTTGTGCTGGGCACAGCGTCG
+@SRR554369.70 70/2
+AAAAGTGCCGCGAGCATGGGCCAGGCANNNNTTTAGTGTGAAGTTTTGCTGAAATAAATACGTATTTTCGCTTAAAATGGATTGTATCGCTGAGTTAAAC
+@SRR554369.71 71/2
+TGCCTGAAATTGTTCAGAACCTGATGCNNNNGGCTCCCACTACACACTTCGTGTCCCTGGGGCAGGCCATCTTGTTCCGGGGGGCTGGCATTGAAACCGT
+@SRR554369.72 72/2
+TATGGACCGGTACGCGCGTTTGCCCAGNNNNTGCTGGCCAGCCGCATGGGTATTCAGGTGCAGTTCTATGAGCCGTCTTTGGGTGAGGGCATGGCCAGCC
+@SRR554369.73 73/2
+GAGGCTCTCGAGCCTAGCGGCGTAATCNNNNGCCTCTCGTTCGGCATCGCGCCGCGGAACAAGGAAGCCGCAGTGGGCAGAGACCAGTTCTGCGTGACCG
+@SRR554369.74 74/2
+GTGACGGAAAACCTGAGCCTGGCCGAANNNNTCCAGCGCGAAGTAGACTCCAGCTCCGTCATGGTGAACCTGCCTACCTGTTTTGCCGACGGCTTCGAGT
+@SRR554369.75 75/2
+AAGGGTTTACCCTCTGTTTTGGCCTAANNNNCTTGTTCACCCTGAGCCGCAGGCCTATATTGGAAACACACATTGATGCATCGCAGCCCTGCCTCTCCAA
+@SRR554369.76 76/2
+CATAGACAATTCAAGCCAAAATAACTGNNNNGAATATCTTACGGCTCGCCTAGACCCCAGGCACCCTTGAAAACTCCTTTTTCACCCATTTGAGTACAAA
+@SRR554369.77 77/2
+TGAGCCGTTCTCTATACCAAAGAAGAGNNNNTAAATGAATGTGCACATAGGTGTAGGATCTCCTCTTAACAAATGGGTTAGCAATGCTTGAAGCGGGTAA
+@SRR554369.78 78/2
+TCCAATAGCGACAACCGGTTTGGAGCGNNNNGCTGATATGCCAACCATTCCAACAGTGGCAGAGGCCGGCTACCCTGGTTTTATTGCACTAAATTGGTAT
+@SRR554369.79 79/2
+TATGCTCCAGCAGTTCCCCTTGATATGNNNNCATAGCGGCATCTAACCTTGTTCAGTTAAGCCAGCAATAGGGCGGTTTCAGTCCGACGGATTGTCTCTT
+@SRR554369.80 80/2
+ATACCACCTTGGCGGTGATTGGCATCANNNNCATGTTGCACTCGGTGCGTAAAGGGCCGGACGAGGCTGGCGAGACCGCCACACCTTCCGCTTTGTCTTA
+@SRR554369.81 81/2
+AGATGTAAGGGCCCTGAGCGCGTTCGANNNNGCACGGGGTGCCGCCCACGGAACCGAAGGCACGGACGGGCGAGTTGACGCCGCCGGGGATGACTTTGCA
+@SRR554369.82 82/2
+TCCCGCTTCTTCCCGGAGTGGTCAGCANNNNACTGGGTTAACCGTCAGTTGTTGGTGGCCGTGCAGGAATGGCGGACCAGCTCTCGCGAGCTCGGCGCAG
+@SRR554369.83 83/2
+GTACGCCTTTGGGGATGAACACAAAAGNNNNATCGGAGAATACGGCCGAGTTCAGGGCGGCGTAGAAGTTGTCGCTAGGAGGGACAACCGTACCCAGATA
+@SRR554369.84 84/2
+CGGAACCCCGGGAAATTTCTGGACACANNNNATACTCTTTGATTGAAGATTGAAGGGCTTTGAGTACAATCGGCAGCTAATTACAGCTTTTTTAAGACGT
+@SRR554369.85 85/2
+AAGCTTGCGACACGGGCATGGCGGCAGNNNNGCCACGACTGATTTCCAGCGCCCCCAAGGTGACGTAGCTGTCGCGCTCGTACTGACGGCGCAACTGCAC
+@SRR554369.86 86/2
+GTGGGGTCAGTGCCAGCAGGGCCAGACNNNNTGCCAGAGCGCTGGCCGTCAGGCCAGTTAGTGCGCCCATATACAGGAAGGGGCGGCGTACAAAGGCGTC
+@SRR554369.87 87/2
+TCAACGTCAATCCCGTGGTGCTCGGACNNNNCTTGCCTTTGCTGTGCGGCTCGACGGCGCGCGCCGCCCTCCTCGTGAATTCGGTGGGGGCACCGCGGGT
+@SRR554369.88 88/2
+CTTCGCGTTTATAAGAATTTAGAAAAANNNNGGCATGCTGTTCTAACGTTGTGGCAGCAAGCTTTTTGCCGAGTTTTCCGGCGCGATCCGTCAATCCTGC
+@SRR554369.89 89/2
+GAATTATCCTTGAACGTCATTCGTCGTNNNNGCGAGCAACTAGGCCCCGACTTCCCGATTATTGGTGTGGGTGGTATTGAATCTGGCCGTCAGGCTCAGG
+@SRR554369.90 90/2
+GGACACTATGACGTGGATACTGCACAGNNNNGCAAAACCAGCACAGGCCGCGACTACGCCGTGCTGAACTACAGCCGTACTTTCAAGAAAGACGGCAAGG
+@SRR554369.91 91/2
+CGAGCACCCACTCGCCGATCTGCCCGANNNNCCCGGACTTTTCCGCCAGCGGCAGGAACTGGCCGAGGACTTATAGCCCCGGTTGTGGTTGACGCAATTC
+@SRR554369.92 92/2
+GCTTCTACAATTGCCCGGCCGGCTGGANNNNCGAGCTGGAGAACAGCGAGATGCTGAAAAGCTACGGCCTGGAGGAGACGTTCACCAATTTCCGTCCGGG
+@SRR554369.93 93/2
+GTGTGTACAAGACCCGGGAACGTATTCNNNNCGACATTCTGATCCGCGATTACTAGCGATTCCGACTTCACGCAGTCGAGTTGCAGACTGCGATCCGGAC
+@SRR554369.94 94/2
+AGGGAACCCTGCCGCGGACAGGATTAGNNNNAGTGAGAGGCGGCCATTCATGTCCACCAAAGCAAAACAACAGAGCAGCCAGCAGATGACCCGCGGCTTC
+@SRR554369.95 95/2
+AAAGTTCTCAGCATGTCAAGGCCAGGTNNNNTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAG
+@SRR554369.96 96/2
+GCGCTACCCAGACACTGCCCCTGATTTTNNNTCAGCTATCTCACCGTTGGGAAATCTCAATCTCAGCCTATTGACAATCTATAGTT
+@SRR554369.97 97/2
+ACTGGCGCTGAAAAGCTTCCTCCCGGCNNNNGAGGAGCATTACCGGATTCTCCTCGACTACGAGCGTCAGGCGCAGGGCTGGGGTTACCCGGAATTCGCC
+@SRR554369.98 98/2
+CCTGCGGTAACGCGGACGCCTGTTCTANNNNGGGCGCGGAATTTCCATCGGAACGCTGTGGCCTGATCCGCGGTCCATGCAGTCCAATCGATGACGGGCT
+@SRR554369.99 99/2
+CGAGGTTTCGCCGCGCGCAGGGTCGGCNNNNCAAAACGGCGTTGTTATACTCGCCCGCACATTCACCGCTGCCAGCACAAAGGATTCGTCCATGAAAGCA
+@SRR554369.100 100/2
+AAATATGCTTCATCTCCAGCTCGAACANNNNCGGATTCGTGAAGATGTCACGACGGCAGCGATAGACGCCTGTTTCTTGGTTTTCTTCCAGGGCGGGATC
diff --git a/util/test_2.fasta.gz b/util/test_2.fasta.gz
new file mode 100644
index 0000000000000000000000000000000000000000..45ffaa158f4a25effd2fec4df192ece5f5e20ede
GIT binary patch
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diff --git a/util/test_script.sh b/util/test_script.sh
index 887c364..72b737c 100755
--- a/util/test_script.sh
+++ b/util/test_script.sh
@@ -2,25 +2,35 @@
 
 set -e
 
-./spring -c -i ../util/test_1.fastq -o abcd 
+./spring -c -i ../util/test_1.fastq -o abcd
 ./spring -d -i abcd -o tmp
 cmp tmp ../util/test_1.fastq
 
+./spring -c -i ../util/test_1.fasta -o abcd --fasta-input
+./spring -d -i abcd -o tmp
+cmp tmp ../util/test_1.fasta
 
-./spring -c -i ../util/test_1.fastq ../util/test_2.fastq -o abcd 
+./spring -c -i ../util/test_1.fastq ../util/test_2.fastq -o abcd
 ./spring -d -i abcd -o tmp
 cmp tmp.1 ../util/test_1.fastq
 cmp tmp.2 ../util/test_2.fastq
 
+./spring -c -i ../util/test_1.fasta ../util/test_2.fasta -o abcd --fasta-input
+./spring -d -i abcd -o tmp
+cmp tmp.1 ../util/test_1.fasta
+cmp tmp.2 ../util/test_2.fasta
 
-./spring -c -i ../util/test_1.fastq -o abcd -l 
+./spring -c -i ../util/test_1.fastq -o abcd -l
 ./spring -d -i abcd -o tmp
 cmp tmp ../util/test_1.fastq
-
 ./spring -d -i abcd -o tmp.gz -g
 gunzip -f tmp.gz
 cmp tmp ../util/test_1.fastq
 
+./spring -c -i ../util/test_1.fasta -o abcd -l --fasta-input
+./spring -d -i abcd -o tmp
+cmp tmp ../util/test_1.fasta
+
 ./spring -c -i ../util/test_1.fastq ../util/test_2.fastq -o abcd -l
 ./spring -d -i abcd -o tmp
 cmp tmp.1 ../util/test_1.fastq
@@ -31,6 +41,11 @@ cmp tmp.2 ../util/test_2.fastq
 cmp tmp.1 ../util/test_1.fastq
 cmp tmp.2 ../util/test_2.fastq
 
+./spring -c -i ../util/test_1.fasta.gz ../util/test_2.fasta.gz -o abcd -g --fasta-input
+./spring -d -i abcd -o tmp
+cmp tmp.1 ../util/test_1.fasta
+cmp tmp.2 ../util/test_2.fasta
+
 ./spring -c -i ../util/test_1.fastq.gz -o abcd -g
 ./spring -d -i abcd -o tmp
 cmp tmp ../util/test_1.fastq
@@ -50,7 +65,7 @@ gunzip -f tmp.2.gz
 cmp tmp.1 ../util/test_1.fastq
 cmp tmp.2 ../util/test_2.fastq
 
-./spring -c -i ../util/test_1.fastq -o abcd -t 8 
+./spring -c -i ../util/test_1.fastq -o abcd -t 8
 ./spring -d -i abcd -o tmp -t 5
 cmp tmp ../util/test_1.fastq
 
@@ -63,18 +78,18 @@ cmp tmp.2 ../util/test_2.fastq
 ./spring -c -i ../util/test_1.fastq -o abcd -r
 ./spring -d -i abcd -o tmp
 sort tmp > tmp.sorted
-sort ../util/test_1.fastq > tmp_1.sorted 
+sort ../util/test_1.fastq > tmp_1.sorted
 cmp tmp.sorted tmp_1.sorted
 
 
 ./spring -c -i ../util/test_1.fastq ../util/test_2.fastq -o abcd -t 8
 ./spring -d -i abcd -o tmp -t 5
 sort tmp.1 > tmp.sorted
-sort ../util/test_1.fastq > tmp_1.sorted 
+sort ../util/test_1.fastq > tmp_1.sorted
 cmp tmp.sorted tmp_1.sorted
 sort tmp.2 > tmp.sorted
-sort ../util/test_2.fastq > tmp_1.sorted 
+sort ../util/test_2.fastq > tmp_1.sorted
 cmp tmp.sorted tmp_1.sorted
 
 echo "Tests successful!"
-rm abcd tmp*
+rm -r abcd tmp*