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R3
legacy
bedtools2
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5a79210e5b40b025974fe122aba005a1fb2eaab1
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8
brentp-fisher-include
jmarshall-warnings3
map-pfm
master
default
merge-assume-stdin
nkindlon-master
nkindlon-master2
pfm_merge
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12
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added new jaccard tool. see PMID: 22693437
add "first" and "last" as new groupby options
80 char
refactor VCF auto-detection
80 char width
80 char width
80 char width
avoid -hist overflow
formatting
tweak healp for -split. cheers to @brentp for the nice addition
support for extracting blocked BED records in fastaFromBed
Merge pull request #28 from brentp/getfasta
allow - to be specified for stdout fasta
change -exons to -split. add tests that make sense.
start of test for -exons arg
errant debug
start of allowing to get concatenated sequence of exons
missing include
Prefer list over vector chromsweep's cache. Huge performance increases
80char cleanup of merge.
clear closest list if an overlap in closest
standardize tag reporting for bamtobed
Merge pull request #27 from nathanweeks/master
If "tac" doesn't exist (e.g., on non GNU/Linux systems like OS X & other BSDs), emulate with sed '1!G;h;$!d' (from http://www.catonmat.net/blog/sed-one-liners-explained-part-one/)
sockaddr_in and sockaddr_in6 are defined in netinet/in.h, which may or may not be included by arpa/inet.h (per POSIX.1-2008). Explicitly include netinet/in.h to compilation on FreeBSD 9.0.
exit is inout BAM file is not found
Merge pull request #26 from brentp/groupby_header
let groupby handle a header line (starting with "#") as do other
fix corner case in chrom sweep. addresses GC issue #141
complement warns to stderr.
send warning to stderr.
remove comment
Merge pull request #25 from brentp/groupby-columns
add tests for groupby
use TokenizeColumns in groupBy and add lineFileUtilities as dependency to Makefile
add TokenizeColumns function
extraneous tab for windowbed -c
try reqs file
add pybedtools req. for docs
add plot_directive
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