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Pull requests list

Add batchx code
#380 by idelvall was merged Jun 7, 2022 Loading…
return 0
#300 by brentp was merged Apr 11, 2019 Loading…
link to smoove
#290 by brentp was merged Feb 13, 2019 Loading…
count total number of aligned reads inside of lumpy_filter
#284 by brentp was merged Jan 8, 2019 Loading…
1
Only include paired-end sequencing reads in discordants file
#279 by ernfrid was merged Nov 27, 2018 Loading…
6
Change inline functions to static inline
#273 by ernfrid was merged Oct 3, 2018 Loading…
match behavior of extract_sv_reads and samblaster
#272 by brentp was merged Oct 2, 2018 Loading…
Changes to get NM in output BAM.
#271 by ernfrid was merged Sep 26, 2018 Loading…
3
use some cram decode stuff to reduce run-time of lumpy_filter for cram
#269 by brentp was merged Sep 11, 2018 Loading…
2
exclude reads that are unmapped, not primary, failing-qc, duplicate
#237 by brentp was merged Apr 4, 2018 Loading…
support cram in lumpy filter
#234 by brentp was merged Feb 7, 2018 Loading…
use max_depth param for svtyper
#189 by brentp was closed Apr 21, 2017 Loading…
filter.c: check return value of sam_read1.
#187 by brentp was merged Apr 21, 2017 Loading…
0.2.13 cram support
#186 by cc2qe was merged Apr 21, 2017 Loading…
dont append when splitting and clean-up gen-vcfs
#180 by brentp was closed Apr 21, 2017 Loading…
dont append when splitting and clean-up gen-vcfs
#179 by brentp was closed Mar 22, 2017 Loading…
lumpy_smooth: default temp directory to $TMPDIR as found by mktemp
#178 by brentp was merged Mar 17, 2017 Loading…
test svtyper. allow specifying -n name of vcf output.
#177 by brentp was merged Mar 13, 2017 Loading…
lumpy_smooth: dont run lumpy_filter if .disc and .split bams exist
#176 by brentp was merged Mar 13, 2017 Loading…
Par filter
#174 by brentp was merged Mar 13, 2017 Loading…
Update README.md
#173 by mschatz was merged Mar 13, 2017 Loading…
1
Make all lumpy python scripts python2.7 and python3 compatible
#163 by mvdbeek was merged Jun 14, 2018 Loading…
2
Parallelize svtyper by variant
#157 by brentp was merged Dec 13, 2016 Loading…
1
restore spaces when checking for file ext
#151 by brentp was merged Nov 22, 2016 Loading…
add svtyping to lumpy_smooth
#150 by brentp was merged Nov 16, 2016 Loading…
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