Mercurial > repos > peterjc > count_roi_variants
changeset 13:4554d79f238b draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
| author | peterjc |
|---|---|
| date | Fri, 09 Nov 2018 10:46:50 -0500 |
| parents | 2429bebcab13 |
| children | 1446811c3fe8 |
| files | tools/count_roi_variants/count_roi_variants.py tools/count_roi_variants/count_roi_variants.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/tools/count_roi_variants/count_roi_variants.py Tue Jun 06 10:17:51 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.py Fri Nov 09 10:46:50 2018 -0500 @@ -85,7 +85,7 @@ def decode_cigar(cigar): - """Returns a list of 2-tuples, integer count and operator char.""" + """Return a list of 2-tuples, integer count and operator char.""" count = "" answer = [] for letter in cigar: @@ -105,12 +105,12 @@ def align_len(cigar_ops): - """Sums the CIGAR M/=/X/D/N operators.""" + """Sum the CIGAR M/=/X/D/N operators.""" return sum(count for count, op in cigar_ops if op in "M=XDN") def expand_cigar(seq, cigar_ops): - """Yields (ref_offset, seq_base) pairs.""" + """Yield (ref_offset, seq_base) pairs.""" ref_offset = 0 seq_offset = 0 for count, op in cigar_ops:
--- a/tools/count_roi_variants/count_roi_variants.xml Tue Jun 06 10:17:51 2017 -0400 +++ b/tools/count_roi_variants/count_roi_variants.xml Fri Nov 09 10:46:50 2018 -0500 @@ -96,7 +96,7 @@ Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16), 2078-9. -http://dx.doi.org/10.1093/bioinformatics/btp352 +https://doi.org/10.1093/bioinformatics/btp352 Peter J.A. Cock (2016), Count sequence variants in region of interest in BAM file. http://toolshed.g2.bx.psu.edu/view/peterjc/count_roi_variants