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Pull requests: arq5x/lumpy-sv

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Pull requests list

update pairend_distro.py to discard outliers
#37 by tabbott was merged Sep 11, 2014 Loading…
1
Initialize SV_BedpeReader::distro_size in constructor
#55 by tjjjohnson was merged Feb 5, 2015 Loading…
1
Add make command to yaha doc and correct binary path
#59 by arahuja was merged Mar 3, 2015 Loading…
added sort order tag to test BAM headers. Also made the files much small...
#62 by cc2qe was merged Mar 3, 2015 Loading…
LUMPY Express, VCF output
#57 by cc2qe was merged Feb 27, 2015 Loading…
make bin directory if it doesn't exist
#60 by cc2qe was merged Mar 3, 2015 Loading…
bump bamkit
#78 by cc2qe was merged May 3, 2015 Loading…
temporarily remove -B only from lumpyexpress examples
#75 by cc2qe was merged Apr 28, 2015 Loading…
add dependency version info issue per #80
#81 by cc2qe was merged May 18, 2015 Loading…
Readme
#65 by cc2qe was merged Apr 3, 2015 Loading…
completed one-sided inversion output as BND
#85 by cc2qe was merged Jun 2, 2015 Loading…
1
Fix for streaming to pysam in bamfilterrg
#116 by chapmanb was merged Jan 21, 2016 Loading…
3
Enable BAM streaming to bamfilterrg for samtools
#117 by chapmanb was merged Jan 21, 2016 Loading…
1
Show evidence command line option ('-e') was not working properly.
#122 by pcingola was merged Apr 15, 2016 Loading…
1
Ignore sparse libraries (<0.1% of BAM)
#125 by cc2qe was merged May 31, 2016 Loading…
update cnvnator_to_bedpes.py to take cnvkit input
#130 by brentp was merged Jul 26, 2016 Loading…
allow specifying depth (cnv calls) to lumpy express with -d $sample_i…
#131 by brentp was merged Aug 7, 2016 Loading…
2
Modifications to #131
#133 by jburatti was merged Aug 17, 2016 Loading…
bump bamkit
#135 by brentp was merged Aug 17, 2016 Loading…
Tests
#137 by brentp was merged Aug 17, 2016 Loading…
remove nounset as it results in an error instead of showing help.
#134 by brentp was merged Aug 17, 2016 Loading…
require log2(FC) > 0.2 for CNS
#136 by brentp was merged Aug 17, 2016 Loading…
Minor additions
#139 by mmterpstra was merged Oct 29, 2016 Loading…
3
Exit with status zero on normal termination
#8 by bpow was closed May 15, 2013 Loading…
1
Typo fixed
#11 by roryk was merged May 15, 2013 Loading…
2
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