Pass variants with no DP information.

This release passes variants that are missing DP information instead of crashing when encountering such a variant. A warning will be emitted for each such variant encountered.

fixing a logic error

Merge pull request #7 from GruA/master

Update mapq0_vcf_filter.sh

bugfix - pysam incompatibility

the newest version of pysam has some incompatibilities with pysamstats. Pinning to the older version fixes that.

Revamped algorithm

Now explicitly pulls MQ0 for every site, instead of relying on existing values, and also uses the tumor samples DP, rather than that from the INFO field. This results in improved filtering - more sites removed.

dockerhub compatibility

Builds which succeed on other machines fail on dockerhub until cython is manually installed. This release does so.

CRAM support

• Now supports cram files
• pinned pip package versions
• updated GATK link to new repo

bugfix for scoping issue causing no filtering

Merge pull request #2 from genome/fix

fixes scoping problem that prevented filtering

handle both zipped and unzipped vcfs

v0.3

cleaning up syntax

bugfix for vcfs where every variant already has MQ tag

Merge pull request #1 from genome/bugfix

input is expected to be gzipped - handle that in edge case