This PR fixes the following problem reported by Nick:
For data where there is a large indel being reported in the VCF, the indel isn't being applied to the consensus as the region is part-covered by a mask and bcftools silently ignores it.
This PR does the following:
adds test data, including some reads that produce an INDEL against the nCov reference
adds a functional test to catch a case when an INDEL is currently being dropped by bcftools
the above test required a bit of code shuffling in artic/pipeline.py, moving the parser to it's own function so that functional tests can call it easily (I also removed some unused imports)
separates unit tests from functional tests by file extension (xxx_unit_test.py and xxx_medaka_test.py) and updates travis to reflect this
updates minion.py so that input to longshot is tabix indexed, this was required for the tests to work as the subset of reads only covered a small portion of the reference genome
updates make_depth_mask.py to fix the reported INDEL dropping problem:
removes existing function that calls samtools depth
replace with a call to mpileup via pysam
add option to include query deletions in reference position counts, such that the depth of coverage for any genome position covered by a deletion is incremented
update the CLI for the artic_make_depth_mask command so that you can replicate the old behaviour (using pysam) with --ignore-deletions
This PR fixes the following problem reported by Nick:
This PR does the following:
artic/pipeline.py
, moving the parser to it's own function so that functional tests can call it easily (I also removed some unused imports)xxx_unit_test.py
andxxx_medaka_test.py
) and updates travis to reflect thisminion.py
so that input to longshot is tabix indexed, this was required for the tests to work as the subset of reads only covered a small portion of the reference genomemake_depth_mask.py
to fix the reported INDEL dropping problem:samtools depth
pysam
artic_make_depth_mask
command so that you can replicate the old behaviour (using pysam) with--ignore-deletions