cancerit PCAP-core issues

cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

GNU General Public License v2.0

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issues

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Hotfix/1.7.1

#72 ThomasSClarke closed 3 months ago
0
Feature/hts update

#71 ThomasSClarke closed 3 months ago
1
a installation error

#70 wul99 opened 2 years ago
0
fix yaml parse RG ID bug

#69 ddomenico opened 2 years ago
0
debug

#68 xcpanda opened 2 years ago
0
Feature/bwakit

#67 keiranmraine closed 3 years ago
0
bam_stats fails to give informative error on BAMs with no RG lines/tags

#66 leovam opened 3 years ago
8
Feature/bwamem2

#65 keiranmraine closed 4 years ago
2
build with libdeflate

#64 mflevine closed 4 years ago
1
WIP: Release/5.4.0

#63 keiranmraine closed 4 years ago
1
Feature/illumina fastq names

#62 keiranmraine closed 4 years ago
1
Is it worth breaking up bwa_mem.pl into more steps?

#61 jsmedmar closed 4 years ago
3
bwa_mem.pl - bwamem step needs to delete bamsort tmp files if retry

#60 keiranmraine closed 4 years ago
1
Expose fastcollate option

#59 keiranmraine closed 4 years ago
0
Feature/full read collate

#58 keiranmraine closed 4 years ago
0
WIP DO NOT MERGE - Hotfix/5.0.5

#57 davidrajones closed 4 years ago
3
Support for Illumina-style paired FASTQ names and related tests

#56 ckandoth closed 4 years ago
1
WIP: DO NOT MERGE - Hotfix/5.0.4

#55 davidrajones closed 4 years ago
1
Feature/bwamem2

#54 keiranmraine closed 4 years ago
5
support for irods: protocol

#53 mgcam opened 4 years ago
0
does the output depend on the input file format?

#52 mgcam closed 4 years ago
3
Changes required to provide a merging script which is aware of mmQc

#50 keiranmraine closed 4 years ago
7
Feature/dockerise

#49 keiranmraine closed 5 years ago
1
C: Makefile should work with htslib installation

#48 keiranmraine opened 5 years ago
0
should not use '\t' as header separator

#47 byb121 opened 5 years ago
0
mapped merge

#46 keiranmraine closed 4 years ago
3
bwa_mem.pl -p stats not doing anything on new versions

#45 jsmedmar closed 5 years ago
8
Support for Illumina's FASTQ file format

#44 ckandoth closed 4 years ago
3
Update Ubuntu 16 install

#43 mflevine closed 5 years ago
1
bamsort sortthreads

#42 mflevine closed 5 years ago
1
map_threads should use all cores if possible

#41 jsmedmar closed 5 years ago
1
Speed up job resume (Threaded.pm)

#40 keiranmraine closed 5 years ago
2
fragment variable usage is inconsistant

#39 keiranmraine closed 5 years ago
1
Hotfix/4.3.1

#38 ghost closed 5 years ago
2
Do Not Merge!: Update CHANGES and bump version

#37 ghost closed 5 years ago
1
Feature/mm flag modifier

#36 ghost closed 5 years ago
0
Hotfix/4.2.7

#35 keiranmraine closed 5 years ago
2
Hotfix/4.2.7

#34 keiranmraine closed 5 years ago
0
Hotfix/4.2.7

#33 keiranmraine closed 5 years ago
1
Hotfix/4.2.7

#32 keiranmraine closed 5 years ago
0
Move sync after chmod

#31 keiranmraine closed 5 years ago
3
Threaded.pm - thread_join_interval

#30 keiranmraine closed 5 years ago
1
Improve yaml to make paired read processing more robust

#29 keiranmraine opened 5 years ago
1
DO NOT MERGE!! Hotfix/4.2.5

#28 ghost closed 5 years ago
2
WIP: Makes bas output more logically comparable to pre 4.1.x release outputs

#27 keiranmraine closed 6 years ago
2
cover: command not found

#26 WortJohn closed 6 years ago
1
fragment parameter has no default although it's listed as optional

#25 jsmedmar closed 6 years ago
0
“multiple target patterns. Stop.” when installing PCAP

#24 Liulab closed 5 years ago
1
add psmisc to install dependencies

#23 jsmedmar closed 6 years ago
5
CI: Add small exec of fq, bam and cram

#22 keiranmraine opened 6 years ago
4