v2.24

• Cadabra now filters somatic calls with a low odds ratio by default. Use param --oddsr to adjust.

v2.23

• Fix for rare contig too long crash problem

v2.22

• Disable GKL by default - appears to still cause instability in some cases

v2.21

• Added option --no-edge-ci to prevent reads from being output with complex indels at the read edges. This allows Manta to run to completion on ABRA2 generated BAM files.

• Removed option for ignoring bad assemblies - this should no longer be necessary.

• Enable Genomics Kernel Library by default for faster compression / decompression

• Added experimental option --ujac for using junctions as contigs. Use of this option can potentially increase compute resource requirements dramatically.

v2.20

• Corrected realignment reproducibility problems. Run to run variation should now be eliminated.

v2.19

• Added MNP support to SimpleAlleleCounter

v2.18

• Allow multiple ABRA2 runs against the same BAM file (by avoiding PG record id collisions)
• Handle leading inserts in Semi-Global alignment properly - was causing invalid SAM records in rare cases.

v2.17

• Memory corruption and leak fixes
• Corrected minor assembly issue related to non-condensed final node
• Increased MAX_SAMPLES to 16

v2.16

• Added SimpleAlleleCounter
• Added script for filtering indels adjacent to introns post-hoc (filter_intron_adjacent_indels.py)

v2.15

• Added option --ignore-bad-assembly to skip over regions with corrupted assembly. See: #18