gt1 biobambam2 issues - Githubissues

gt1 / biobambam2

Tools for early stage alignment file processing

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`bamsormadup` stalls if temp folder does not exist

#79 fgvieira closed 5 years ago
4
bammarkduplicates - unusual case

#78 keiranmraine closed 5 years ago
2
bamsormadup v2.0.79: assertion failed

#77 fgvieira closed 5 years ago
2
does bamtofastq have same outputs for queryname and coordinate sorted input BAM/CRAM

#76 djomlaart closed 5 years ago
2
Correct docs PGID -> RGID

#75 EvanTheB closed 6 years ago
1
failed to find libmaus2

#74 kemin711 opened 6 years ago
8
Feature request: bamsormadup quality filter

#73 matthdsm opened 6 years ago
0
bamsort: Query name contains illegal symbols

#72 mmokrejs opened 6 years ago
0
bamsort crash at libmaus2::lz::BgzfDeflateParallel::flush

#71 mmokrejs opened 6 years ago
4
bamsort-2.0.87: input reading gets stuck

#70 mmokrejs opened 6 years ago
0
Invalid @PG line

#69 SergejN opened 6 years ago
0
Is REF_PATH/REF_CACHE used for reading CRAM?

#68 keiranmraine opened 6 years ago
1
Controlling number of temporary files for bamsormadup

#67 chapmanb opened 6 years ago
0
Support for positions values up to 2^31 (=according to BAM spec) instead of 2^29

#66 WimSpee opened 6 years ago
5
csi indexing of BAM file

#65 keiranmraine closed 6 years ago
3
2.0.83 - precompiled archive duplicated content

#64 keiranmraine closed 6 years ago
1
bammaskflags - add condition option?

#63 keiranmraine closed 6 years ago
2
bammerge - additional decompression threads?

#62 keiranmraine opened 6 years ago
0
Invalid alignment: Query name contains illegal symbols

#61 mmokrejs opened 6 years ago
0
query: bammarkduplicates2 - are QCfail included

#60 keiranmraine closed 6 years ago
2
Any Option for bamsort in Parallel?

#59 spikeliu opened 6 years ago
6
bamcollate2 not reporting all reads

#58 mirahan opened 6 years ago
2
bamtofastq - output ordering

#57 keiranmraine closed 6 years ago
2
bam2fastq failed

#56 lmanchon opened 6 years ago
8
bammarkduplicates vs bammarkduplicates2 documentation

#55 jeffbhasin opened 6 years ago
3
libmaus2 detected but gives can not compile error in configure script

#54 jeffbhasin closed 6 years ago
4
Installation Error. "programs/bamadapterfind.cpp: using ‘typename’ outside of template"

#53 yuankunzhu closed 6 years ago
2
Feature request: split by chromosome

#52 jasper1918 opened 6 years ago
2
disablevalidation option for bammerge possible ?

#51 af8 closed 6 years ago
5
"Too many open files"

#50 map2085 opened 6 years ago
4
incomplete pairs

#49 nesilin closed 6 years ago
2
FYI: biobambam2 on dockstore.org

#48 keiranmraine opened 7 years ago
0
bamcollate2 - segfaults

#47 keiranmraine closed 7 years ago
2
bammerge: Accept wildcard regexp when parsing I= input

#46 mmokrejs opened 7 years ago
2
Do not crash if no argument was provided

#45 mmokrejs opened 7 years ago
1
Conflicting executable names

#44 sjackman closed 6 years ago
7
bamtofastq

#43 nesilin closed 7 years ago
2
Not working on Centos7 –libmaus2 related error

#42 akhats closed 7 years ago
4
Improving documentation and commandline argument names/behavior

#41 mmokrejs opened 7 years ago
0
No adapter clipping if remaining sequence would be a single base.

#40 whitwham closed 7 years ago
1
bamclipreinsert error when the sequence contains a single base with a quality of 9

#39 srl147 opened 7 years ago
4
bammarkduplicates2 - improving throughput

#38 keiranmraine opened 7 years ago
0
bamtofastq - is multi-thread possible?

#37 keiranmraine opened 7 years ago
0
bammarkduplicates piping to stdout problem

#36 steffenheyne closed 7 years ago
2
bamsormadup bin size errors with SAM input from bwa

#35 chapmanb closed 7 years ago
2
Empty MC:Z tags from bamsormadup in 2.0.57

#34 chapmanb closed 7 years ago
2
High memory usage for bamsormadup on inputs with many reference contigs

#33 chapmanb opened 7 years ago
2
Question - bammarkduplicates2 - does it invoke 'top'?

#32 keiranmraine closed 7 years ago
2
Added an explicit iRODS disconnect to avoid the iRODS 4.19 crash.

#31 whitwham closed 7 years ago
0
Specifying parameters on the command line

#30 markmcdowall closed 7 years ago
3