v0.97c

Fix to deletion detection in SomaticLocusCaller

v0.97b

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

v0.97

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

v0.96

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

v0.95

• 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).

v0.94

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

v0.92

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

v0.91

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)

v0.86

Improved stability in the face of "noisy" assemblies. Issues with using too much memory are reduced.
Various improvements to Cadabra - a somatic indel caller for ABRA alignments.
Various minor tweaks and bug fixes.

v0.82

Minor bug fixes and better default param settings.