Codestin Search App

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

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.

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

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.

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

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

Releases: mozack/abra2