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3.5.0

  • Adds RNA downloads to PanCancer download tool gnos_pull.pl
  • Hardening of external process handling in PCAP::Threaded
  • Adds C version of diff_bams

3.4.0

  • Significant speed up of BAM generation under bwa_mem.pl by using separate process to do compression of mark duplicate output and streaming BAS generation. Not possible to do this to CRAM in same way.

3.3.4

  • Reduce disk usage when running bwa_mem.pl
  • Improve throughput via slightly unintuitive use of additional pipes

3.3.0

  • adds map_threads|mt option to bwa_mem.pl to allow more control of parallel processing in one shot submission.
  • adds bwa_pl|l option to bwa_mem.pl to allow preload of different malloc libraries.

3.2.0

  • Move from legacy kent bigwig manipulation code and to cgpBigWig
    • Faster and handles the huge number of contigs in many new reference builds.
    • Resulting changes to underlying installed tools is bwcat now bwjoin to be more descriptive of actual function.

3.1.1

Handle recent changes to BioPerl structure

3.1.0

  • Use BWA default for -T previously hard coded to -T 0.
    • Can be passed through bwa_mem.pl other ags to bwa via the -b option.
  • Fix bam2bedgraph compilation since changes to underlying libraries
  • bamToBw.pl - expose read flag filters
  • Drop dependancy on Bio::DB::HTS INSTALL.pl as can't fix to known good version.
  • Added travis CI
  • Add support for output directly to CRAM
  • bwa version upgraded to 0.7.15

3.0.0

  • Threading module now converts currently running step to bash script for following reasons:
    • Changes logging to use file redirects instead of Capture::Tiny - prevent log bleed into wrong files
    • Commands for failed jobs remain after shutdown for easy debug/testing
  • Log and progress file names simplified so more portable.

2.4.1

  • Modified reheadSQ to be more robust.

2.1.0

  • Adds xam_coverage_bins.pl which calculates fraction of targets covered at various depths (BAM/CRAM), using BED/GFF3 as target bait file.

2.0.0

  • bwa_mem.pl
    • allow user to specify BWA mapping parameters
    • now accepts CRAM as input
  • bamToBw.pl - now accepts CRAM as input.
  • bam_stats - Adds 2 new stats:
    • #_mapped_pairs
    • #_inter_chr_pairs
  • Dependancy changes
    • WARNING: ensure all related tools handle these updates
    • samtools, now only uses htslib based versions (1.3+, handling deprecated use of sort)
    • Bio::DB::HTS htslib bindings replacing Bio::DB::Sam

1.14.0

  • bwa_mem.pl - Option to disable duplicate marking

1.13.0

  • bam_stats - Unit tests for C code
  • bam_stats - Fix to median insert size calculation

1.11.0

  • bam_stats - new rna switch to give more appropriate insert size stats
  • bam_stats - more robust handling of optional RG header entries
  • bam_stats - allows streaming IO (thanks to @jenniferliddle)
  • bwa_mem.pl - Handle ' in RG header line/IDs
  • Generally improved version handling and updated versions of some tools.

1.9.1

  • Changed final log folder to include sample name and analysis type, prevents clash when lots of data to same output loc.

1.9.0

  • Fix bugs #52 and #53
  • Modified bwa_mem.pl to accept multi-readgroup BAM as input

1.7.1

  • Turns out BWA mem still requires fixmates to get proper isize distributions
  • bumped biobambam to 0.0.191

1.7.0

  • Switched to bam_stats C in bwa_mem.pl.
  • Updates to bam_to_sra.pl to prevent bad SM values in unaligned BAM uploads.

1.6.0

  • Adding local file mode for sites that cannot download from GNOS when the xml_to_bas.pl script runs
  • gnos_pull.pl - see linked docs

1.5.4

  • bam_stats C
    • Reference file parameter is now optional to replicate bam_stats.pl functionality.
    • Warnings in help, and when a cram file is given as reference from header may not be found, and bam stats will fail.

1.5.3

  • bam_stats C - changed array for khash in insert size calculations in order to make code more robust.
  • Header RG line reading now reads anything not a tab or newline as it should when determining what the values of tags are.

1.5.2

bamToBw.pl fixes

  • Pull actual binaries from jkent_util not html page associated
  • process name corrections in bamToBw.pm command line args

1.5.1

  • bam_stats c now has CRAM support.
  • Also dropped need for samtools v1.x api as can be handled by htslib on it's own.

1.5.0

  • bamToBw.pl and new biobambam dep

No changes to old tools, just additions and prep for handling CRAM input.

1.4.0

bam_stats in C, less than 2 hours to generate stats on a sample level BAM file of ~120GB.

1.3.0

  • bam_stats.pl is now multi-threaded, can get ~50% runtime reduction with 3-4 threads, memory still <500MB.
  • Upgrades biobambam to 0.0.185 (and dependencies).

1.2.3

xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile, #54

1.2.2

Fixed bug in bwa_mem.pl when using '-f' option on paired fastq.

1.2.1

Makes xml_to_bas.pl more robust on AWS. Retrieved XML was being truncated on some network configurations.

1.2.0

Modifications made to the bwa_mem.pl code to split a lane of data into fragments to reduce failure recovery time. Primarily added to handle X10 data better.

Also updated samtools to 0.1.20, last version that is currently compatible with Bio::DB::Sam.

1.1.1

Fix missing dependancy and build a relocatable version of biobambam suitable for use in artifactory.

1.1.0

  • Minor enhancement to bwa_mem.pl to automatically generate the *.bas file.
  • Added xml_to_bas.pl for pancancer users, see the wiki for details.
  • Fixed a few minor issues, #36, #37, #39

1.0.4

  • Install biobambam 0.0.142 to prevent over-counting of duplicates when multiple libraries, also required libmaus 0.0.124.
  • Improve install for those working with multiple perl installs.
  • Improve version inheritance, less code

1.0.3

  • Corrected issue from dynamic de-reference of hash, issue for pre 5.14 perl and potentially unstable in future.
  • Added missing project code to cv terms.
  • Bug-fixed upgrade path, still needs better solution.
  • Cleaned up messaging in Threaded module.

1.0.2

  • Upgrade install to pull biobambam 0.0.138
    • fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.
    • fastqtobam option to relax qscore validation without turning off... careful
  • Upgrade install to pull BWA 0.7.8
    • performance improvements for short read alignment (100bp)

1.0.1

  • Upgrade install to pull biobambam 0.0.135
    • fastqtobam supports Casava v1.8
    • bamsort supports NM/MD correction during sam->bam/merge process
  • Minor enhancement to BAS reader module.
  • Sample name from command line passed through to SM of RG header in bwa_mem.pl
  • SRA.pm - check that rg id is unique within run of code (thanks to Junjun Zhang)
  • Threads.pm - join interval is now configurable.

1.0.0

  • bam_stats.pl actually installed now.
  • Basic *.bas perl access module.
  • Upgraded libmaus/biobambam to resolve patch and CentOS install issue.
  • Reference implementations ensure unique RG:ID between files.

0.3.0

  • Changes for the re-worked PanCancer submission SOP.
  • Patch for libmaus issue as not going to be a release in time.
  • Bug fix for *.info files (bam_to_sra_sub.pl).
  • Added bam_stats.pl.
  • Project is now defaulted when not provided (bam_to_sra_sub.pl).

0.2.0 14-Mar-2014

  • Updated biobambam version
  • Documented additional dependencies
  • Improved install implementation

0.0.2-beta2 04-Feb-2014

  • Updated module naming in preparation for publication to GitHub.
  • Added license boiler plate.
  • bam_to_sra_sub.pl generates valid XML for GNOS, some features disabled until modifications to GNOS can be made (warnings indicate this on execution)

0.0.2-beta 29-Jan-2014

  • Pre release with basic SRA XML generation (GENOS)
  • Updated requirements for biobambam of 0.0.120
  • Tests update to reflect change in biobambam requirement

0.0.1 11-Sep-2013

  • Initial codebase for PanCancer alignment with BWA 0.6.2.