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mskcc / cmo

Command-line tools for data analysts at the CMO
GNU General Public License v2.0
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cmo_fillout now gets sample IDs from BAMs instead of MAF #59

Closed ckandoth closed 7 years ago

ckandoth commented 7 years ago

Note new dependency on pysam to extract sample IDs from BAMs, which are passed into GBCMS, so that it uses proper sample IDs in the fillout output, rather than BAM file basename. cmo_fillout was earlier limiting .fillout.portal.maf output to just the tumor-normals seen in the input MAF. This is problematic in the pipeline where cmo_fillout is called per tumor-normal, and not across the whole cohort.

ckandoth commented 7 years ago

Added ability to pass in a fillout file precomputed by GBCMS. As before, any lines not seen in the input MAF will be tagged with Mutation_Status=None. This can happen if someone mistakenly uses an input MAF with the wrong fillout file. But that's OK - it's just working as advertised.

ckandoth commented 7 years ago

BAM files are now optional if a precomputed fillout is provided. Added pysam as dependency in setup.py, And updated cmo/_version.py to 1.6.10.