adamewing/bamsurgeon v1.1

Bugfixes / cleanups:

error instead of crash if no contigs for left end of translocation 5b3ede6 ignore non-primary reads in target BAM when replacing reads 3d17e97 fix indel bug with long insertions 32b3fae remove instructions with old bwa option b82d384 prevent insertion close to contig edge 54a2499 split actions by semicolon for multi-sv c8256ea shoten mutation id string daa1f85 remove picard 4g memory request 213bd11 handle case where no contigs are generated 6ee1f8e

Features:

add option to ignore input vs output sanity check 310dbbf all option to allow N bases in contigs d28a154 ability to select specific insertions from --inslib 143b6b3 explain single-end error if --single not given 01cd8ee allow per-variant SV VAF adjustment via varfile b096aca