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Bcftools ploidy #133

Merged
merged 32 commits into from
Aug 31, 2016
Merged

Bcftools ploidy #133

merged 32 commits into from
Aug 31, 2016

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martinghunt
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Fxies a few small issues involving het calls and bcftools. Also remove dependenciy on samtools and bcftools, as pysam now used instead of system calls

Martin Hunt and others added 30 commits August 25, 2016 00:00
replace bcftools with own c++ version that keeps minor alleles
70d8335
Remove unneeded tbi file
d3168fb
Depths file has total per contig, no need to total them up
79debe1
Store name of contigs depth file
cd37674
rm contig depths file
61505ab
Update to use new samtools_variants options
60ee502
Remove bcftools
d5ba3a1
Use pysam.faidx instead of syscall to samtools
6a8a274
Remove unused options
002ea3c
Use pysam for mapping instead of syscalls to samtools
910051f
Remove best_seq_chooser, done with mash instead
ccdaadc
Use pysam instead of syscall to mpileup
c770974
Remove samtools dependency (use pysam)
33eff8c
Remove unused imports
129579e
Remove unused import sys
819b930
Remove unused imports
69443ee
Mention required python packages
0637720
require pysam >= 0.9.1
e770715
Min python 3.3.2
b62be43
More persmissive with input format
055b8c4
Remove unused options
2f4a015
faidx first, to stop fa_load messages to stderr
f9bd4d9
Drop max_allele_freq to 90
cbaf51d
Add min sceond allele depth = 2
c5f378c
Bug fix checking second allele depth
14674da
@martinghunt
new method _depths_look_het
6511dd7
@martinghunt
remove debug prints
a7c00b5
@martinghunt
New class attribute is_het
908db38
@martinghunt
Get alt base from ref_ctg_change first if possible
6baa93f
@martinghunt
Add test of whole run of summary
ddc7adc
@martinghunt martinghunt merged commit 07d17b5 into sanger-pathogens:master Aug 31, 2016
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@martinghunt