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Change Log

v1.1 (2019-05-21)

Full Changelog

Implemented enhancements:

  • add needlestack logo in log.info #182
  • add INFO field containing allelic frequency #174
  • Add an option to only plot somatic mutations #149
  • Make the main 3 processes pipe-friendly to avoid intermediate outputs #147
  • Re-write pileup2baseindel.pl in C++ #146
  • Flag possible cross-sample contamination of normal DNA in tumor samples #138
  • Put ./. genotype when there is no power to identify a variant #137
  • Implement Tumor-Normal pair somatic variant calling #133
  • Add alignment plot in the PDF #73
  • Make a script that would run needlestack without nextflow #72

Fixed bugs:

  • max_dp default value in readme is wrong #176
  • --help should exit 0 #161
  • Manage bed specification for both bed and region #157
  • Using renamed symlinks as input BAM files doesn't work with --use_file_name option #152

Closed issues:

  • How to identify each sample? #166
  • Github readme != Docker readme #159

v1.0 (2016-08-03)

Full Changelog

Implemented enhancements:

  • Manage the three possible genotypes in vcf #130
  • The graph showing AF vs log10(qval) should show phred-scaled qvalues #121

Fixed bugs:

  • Contours seem to be incorrect #128
  • correct file name extraction for sample name #126
  • Let min_qval be equal to 0 #119
  • plot improved error rate confidence interval #117

Closed issues:

  • QUAL should not be reported as Inf in VCF when q-value=0 #125
  • Add pipeline execution DAG in README #123

v0.3 (2016-05-03)

Full Changelog

Implemented enhancements:

  • color points by qvalues in regression plot #85
  • Add an option to directly input a region for calling in the command line #71
  • Improve the bed split method #47
  • Change the number of entry in the INFO and FORMAT VCF fields #108
  • Add contour lines for a set of qvalues in the plot #100
  • Add an option to choose output VCF file name (--out_vcf?) #81
  • Change the way we publish new version #69
  • Make the stable docker file more stable #68
  • Add more tests in CircleCI #55
  • Remove unnecessary intermediate outputs #51
  • In the absence of a bed file the pipeline should run on the full reference genome #39
  • Improve R script command line parsing #38
  • Add version numbers in VCF output #20

Fixed bugs:

  • VCF files have to be sorted #110
  • Sometimes large number in VCF files are written in scientific notations #109
  • error when coverage is null for every bam file #99
  • Calling doesn't work when a region contains only T in the reference #96
  • Check that BAM folder contains bam files #66
  • Check if the gzi is present if the ref is gz #65
  • Verify the user inputs are correct #42

v0.2 (2015-10-19)

Full Changelog

Implemented enhancements:

  • Add logo image #62
  • add --no_indel option #56
  • Correct english typos in readme, help and log #53
  • The pipeline randomly crashes with java.nio.file.NoSuchFileException: XXX_empty.pdf #49
  • Add information about the pipeline in the log #41
  • Add program usage when launched with --help #40
  • Change the way chromosome length is calculated #34
  • Option all\_sites should rather be called all\_SNVs #33
  • Choose a better name for the pipeline and change file names accordingly #31
  • Add contigs in VCF header #25
  • Move to IARC-bioinfo organisation repo #22
  • Add a zoomed regression plot #21

Fixed bugs:

  • The pipeline randomly crashes with java.nio.file.NoSuchFileException: XXX\_empty.pdf #49
  • QVAL is wrongly called GQ for indels #36
  • Dockerfile always adds scripts from master branch #27
  • CircleCI deploy.sh doesn't trigger correctly Docker Hub #26

v0.1 (2015-09-18)

Implemented enhancements:

  • Choose strand bias filter to apply #15

Fixed bugs:

  • Pipeline crashed when no variant is found #14
  • Cutting bed files with zero length regions was not working properly #10

* This Change Log was automatically generated by github_changelog_generator