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biod
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sambamba
Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Adding query name sorting as in Picard
#370
TimurIs
closed
5 years ago
1
Feature request - add option to sort by query name like Picard
#369
TimurIs
closed
5 years ago
5
sambamba mpileup with reference
#368
feihongloveworld
closed
5 years ago
1
How to merge temporal files from sort command?
#367
tluquez
closed
5 years ago
2
Fails to build: BioD/bio/maf/reader.d(53): Error: cannot implicitly convert expression
#366
rekado
closed
5 years ago
4
Check mark duplicates for larger numbers
#365
pjotrp
closed
5 years ago
0
Readcount results are shifted for depth calculation when chrom id is not found in bam
#364
hassanfa
closed
3 years ago
7
Error: Implicit string concatenation is deprecated
#363
sjackman
closed
5 years ago
5
Error: read-modify-write operations are not allowed for `shared` variables.
#362
tillea
closed
6 years ago
8
Mark duplicates in files with many contigs
#361
dpryan79
closed
6 years ago
7
sambamba depth with fix-mate-overlaps results in possible overflow
#360
hassanfa
closed
2 years ago
5
Signed/Unsigned
#359
SergejN
closed
3 years ago
12
Travis build is failing
#358
pjotrp
closed
5 years ago
0
BAM output header contains sambamba version info
#357
pjotrp
closed
6 years ago
0
sort removing tags from @RG header
#356
Kurt-Hetrick
closed
5 years ago
1
Upgrade htslib
#355
pjotrp
closed
4 years ago
5
[WIP] Followup submodule refresh for sambamba and TravisCI pass with newer LDC versions
#354
brainstorm
closed
6 years ago
2
view error while filtering 10X BAM file on [CB] tag
#353
RichardCorbett
closed
4 years ago
1
Support BCFtools > 1.4.1
#352
nathanhaigh
closed
6 years ago
1
Not recognising bcftools version >=1.5
#350
nathanhaigh
closed
6 years ago
2
Is sambamba-markdup library aware?
#349
yuankunzhu
closed
5 years ago
4
ref_id in filtering expression
#348
hirokomatsui
closed
5 years ago
0
Error: template std.utf.toUTF8 cannot deduce function from argument types
#347
sjackman
closed
5 years ago
6
sambamba (release 0.6.7) had abnormally finished with error code 35584
#346
gskrasnov
closed
6 years ago
3
sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files
#345
carsonhh
closed
6 years ago
3
Version 0.6.7 fails to build on i386 but version 0.6.6 has build successfully
#344
tillea
opened
6 years ago
9
how to reduce the bam file to different multiplier(5X,10X,15X......)
#343
whiteorchid
closed
5 years ago
2
line 11: 27182 Floating point exception(core dumped)
#342
jflucier
closed
5 years ago
1
add feature "markdup support multiple input bams and argument file"
#341
lituan
closed
4 years ago
2
Assertion failure in `sambamba depth`
#340
hzpc-joostk
closed
5 years ago
2
Clean up error message for sambamba-sort: couldn't parse (Allow memory command line option to be case independent.)
#339
AMChalkie
closed
6 years ago
1
Make no longer builds for macos
#338
pjotrp
closed
5 years ago
4
fix index documentation
#337
mschilli87
closed
6 years ago
1
Index documentation incorrect
#336
stephenwilliams22
closed
6 years ago
4
Intel Xeon bug may segfault Sambamba
#335
pjotrp
closed
6 years ago
1
Add subsampling support
#334
pjotrp
closed
3 years ago
1
Feature Request - file of file name for inputs for programs that take multiple inputs
#333
bwlang
closed
4 years ago
1
Error with make sambamba-ldmd2-64 command?
#332
shreyashruti
closed
6 years ago
1
segmentation fault attempting to view header in json format
#331
pjotrp
closed
6 years ago
1
Markdup v0.6.6 Quits without error
#330
ATpoint
closed
6 years ago
2
undefined reference when trying to make sambamba
#329
najoshi
closed
6 years ago
2
Debug version: SAM output of CRAM file is populated with debug on pipe
#328
hzpc-joostk
closed
6 years ago
3
Sambamba view -F missing '*' character
#327
cshneider-zz
closed
3 years ago
1
Mark Duplicate for Scaffolds
#326
wangshun1121
closed
6 years ago
1
Optical duplicate calculation during markdup
#325
RichardCorbett
closed
3 years ago
2
OSX binaries for 0.6.7 release
#324
cbrueffer
closed
6 years ago
1
Sambamba view is dropping reads when you specify a region
#323
carsonhh
closed
3 years ago
1
sambamba index incompatible with htslib for HTS_IDX_NOCOOR ("*" contig)
#322
ghost
closed
6 years ago
4
Sambamba hangs on a bam file without reads
#321
choesang
closed
6 years ago
2
Failed to build due to undefined reference
#320
changhw01
closed
6 years ago
9
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