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Pre-release

@mozack mozack released this Aug 3, 2016 · 4 commits to master since this release

Fix to deletion detection in SomaticLocusCaller

Assets 2
Pre-release

@mozack mozack released this Jul 18, 2016 · 5 commits to master since this release

Log to stderr allowing bam file to be written to /dev/stdout for streaming.

Assets 3

@mozack mozack released this Jun 20, 2016 · 7 commits to master since this release

  • Allow comments in bed file header - submitted by NoSeatbelts
  • Allow 1 base target regions
  • Added very basic param check in Cadabra
Assets 3

@mozack mozack released this Nov 12, 2015 · 19 commits to master since this release

  • Do not allow kmers to grow boundlessly - this could potentially cause buffer overruns for longer reads.
Assets 3

@mozack mozack released this Nov 11, 2015 · 21 commits to master since this release

  • Fix to Cadabra crashing when first read in chromosome is unmapped.
  • Handle both hard clipping and soft clipping handling at beginning of a read.
  • Additional suppression of logging when in quiet mode (which is still somewhat chatty).
  • Parameterized max_nodes (Workaround for "Graph too complex" issues in noisy samples such as some FFPE cases).
Assets 3

@mozack mozack released this Jul 21, 2015 · 29 commits to master since this release

Improved SV detection
Added --no-debug option for reduced logging to stdout.

Assets 3
Jul 14, 2015
version 0.93

@mozack mozack released this Apr 6, 2015 · 43 commits to master since this release

Patch release. Addressed issue with dropped secondary / supplementary reads.

Assets 3

@mozack mozack released this Mar 20, 2015 · 52 commits to master since this release

This release is mostly related to compute performance with a couple of minor usability tweaks.

Exposed bwa index prefix as optional param distinct from reference fasta.

Graph pruning improvements:

  • Parameterized min edge ratio and increased default to 2% (10% recommended for germline)
  • Use per sample edge ratio instead of aggregate ratio in edge pruning for multi-sample cases

Fixed bug in reading beyond end of reference sequence.

Compute performance improvements

  • More intelligent downsampling for assembly (reduces memory issues in exceedingly high depth cases)
  • Reduced intermediate file I/O - now consuming BWA output directly
  • Upgraded to current picard and htsjdk jars allowing for use of IntelDeflator for BAM compression
  • More efficient SAM record parsing
  • Introduced thread pooling
  • Reduced logging (to some degree)
Assets 3
Mar 17, 2015
version 0.90
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