Support parsing hg38 BAM files with @SQ AH fields

andyrimmer / Platypus

Platypus Variant Caller

GNU General Public License v3.0

105 stars 38 forks source link

Support parsing hg38 BAM files with @SQ AH fields #67

Closed chapmanb closed 6 years ago

chapmanb commented 7 years ago

hg38 BAM headers have alternative loci specified as AH in the @SQ sequence dictionary. This adds support for these during parsing. Otherwise extraction of sequence names from BAM files fails: chapmanb/bcbio-nextgen#1988

jpc2350 commented 6 years ago

@dancooke @andyrimmer Bump - Could this be looked at and Merged please. We are also requiring this code to be merged/fixed and released.