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Het snp reporting #115

Merged
merged 32 commits into from
Aug 2, 2016
Merged

Het snp reporting #115

merged 32 commits into from
Aug 2, 2016

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martinghunt
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  • option in summary to report het snps for known noncoding sequences
  • stop caching with travis. There was a test that relied on spades and passed, but spades wasn't meant to be installed.

martinghunt and others added 30 commits August 1, 2016 09:33
@martinghunt
return dict of scaff names and var positions
1bc1d5f
@martinghunt
variants_in_coords now returns a dict, not bool
fd387c2
@martinghunt
store samtools variants as attribute so can use when making report lines
f25bfe0
@martinghunt
Remove debug print
02c9db6
@martinghunt
Report het snps called by samtools
2ed2455
@martinghunt
Store var coords in a set instead of list
ffe2706
@martinghunt
Test het snp reporting at position of known variant in a gene
26ba92b
@martinghunt
New test test_full_run_ok_samtools_snp_pres_abs_noncoding
7d0b580
@martinghunt
New test test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding
b8a3e55
@martinghunt
add test test_full_run_ok_samtools_snp_var_only_gene
b8e8688
@martinghunt
new test test_full_run_ok_samtools_snp_known_position_var_only_gene_d…
fad1e7c 
…oes_not_have_var
@martinghunt
add test test_full_run_ok_samtools_snp_known_position_var_only_gene_d…
65531a5 
…oes_have_var
@martinghunt
add test test_full_run_ok_samtools_snp_var_only_noncoding
7391e24
@martinghunt
add test test_full_run_ok_samtools_snp_known_position_var_only_noncod…
490c37d 
…ing_does_not_have_var
@martinghunt
add test test_full_run_ok_samtools_snp_known_position_var_only_noncod…
6929d22 
…ing_does_have_var
@martinghunt
Filter HET heterozygous SNP lines
caf5111
@martinghunt
New method _get_known_noncoding_het_snp
433f3fa
@martinghunt
New method known_noncoding_het_snps
f9d5691
@martinghunt
return dict instead of set
26dec15
@martinghunt
Get dict of het snps as well as column names
e214d70
@martinghunt
Get het_snps as well
08874e2
@martinghunt
Bug fix, as now have het snp column
df63496
@martinghunt
Do not put het snps at end of tuple
bc9e91f
@martinghunt
Add option to show known het snps
32bdd87
@martinghunt
Add command line option --het to summary
ce9a05d
@martinghunt
Make suffix '.%'
767e4ba
@martinghunt
Fix het call phandango headings/colours
f4b3a81
@martinghunt
Add NA to % column when not have known snp and are reporting hets
a93927d
@martinghunt
Sanity check number of columns is consistent
fc0167a
bug fix not adding % column for some samples
c70bc90
@martinghunt martinghunt merged commit a342ec6 into sanger-pathogens:master Aug 2, 2016
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@martinghunt