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cancerit
/
cgpCaVEManPostProcessing
Flagging add on to CaVEMan
http://cancerit.github.io/cgpCaVEManPostProcessing/
GNU Affero General Public License v3.0
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Can't use an undefined value as an ARRAY reference
#44
wjaratlerdsiri
opened
1 year ago
0
Feature/mnv flags
#43
davidrajones
closed
2 years ago
1
Feature/yaml config
#42
davidrajones
closed
2 years ago
0
Feature/new flags
#41
davidrajones
closed
2 years ago
2
Feature/circleci
#40
davidrajones
closed
3 years ago
1
Misleading command line help: convertVCFUnmatchedToBed.pl -infile
#38
keiranmraine
opened
4 years ago
0
Change to use low-level api where possible and reduce fetch calls
#37
keiranmraine
closed
4 years ago
1
Feature/strand count bug
#36
keiranmraine
closed
4 years ago
2
Fails if all reads have common call at position
#35
keiranmraine
closed
4 years ago
3
Hotfix/1.8.9 - DO NOT MERGE
#34
ghost
closed
4 years ago
0
WIP: Handle various formats used by VCF to show no data for sample
#33
keiranmraine
closed
5 years ago
1
WIP: Reduce memory overhead of unmatched normal bed by using single shared reference
#32
keiranmraine
closed
5 years ago
1
Discuss: split + index flagging
#31
keiranmraine
opened
5 years ago
0
DO NOT MERGE! Hotfix/1.8.6
#30
ghost
closed
5 years ago
0
downgrades bedtools in error
#29
keiranmraine
opened
6 years ago
0
Feature/overlapping reads
#28
ghost
closed
6 years ago
0
Remove species name from config file
#27
ghost
opened
6 years ago
0
Pre-release tag for fragment analysis
#26
keiranmraine
closed
6 years ago
2
Fixes #18, Fixes #19
#25
ghost
closed
6 years ago
0
Feature/travis testing
#24
ghost
closed
7 years ago
0
Need option so that actually fails when no flaglist found
#23
keiranmraine
closed
6 years ago
1
Perl module missing from Makefile
#22
keiranmraine
closed
7 years ago
1
bedtools not indicated as dep
#21
keiranmraine
closed
7 years ago
0
Require a more robust error on config ini access
#20
ghost
closed
6 years ago
0
ability to create output directory
#19
sb43
closed
6 years ago
1
Ability to override ini file flag list with a commandline
#18
ghost
closed
6 years ago
0
Add use of share dir to config files
#17
ghost
closed
6 years ago
4
All test bed files now bgzipped and with tbi index
#16
ghost
closed
8 years ago
0
Feature/tabix for bed
#15
ghost
closed
8 years ago
2
Feature/biohts conversion
#14
ghost
closed
8 years ago
0
Bio::DB::HTS conversion
#13
ghost
closed
8 years ago
0
t/cgpFlagCaVEMan.t - test fail under perl5.18+
#12
keiranmraine
closed
8 years ago
1
make throws many warnings
#11
keiranmraine
closed
8 years ago
0
Merge clear flags
#10
ghost
closed
8 years ago
0
Feature/clip align soft flags
#9
ghost
closed
8 years ago
0
Feature/test cleanup and vcf bugs
#8
keiranmraine
closed
9 years ago
0
Possible bug: cgpFlagCaVEMan.pl - cgpFlagCaVEMan.t
#7
jwhsanger
closed
9 years ago
10
Possible bug: cgpFlagCaVEMan.pl
#6
jwhsanger
closed
9 years ago
1
Feature/bed unmatched
#5
keiranmraine
closed
9 years ago
0
Typo in help - circular dependencies
#4
ghost
closed
9 years ago
0
Moved some methods round so that pulldown flagging functions
#3
keiranmraine
closed
9 years ago
0
fixes dependency on CGP bedtools path and http access for unmatched normal panel
#2
keiranmraine
closed
9 years ago
0
Merge for PanCancer release
#1
keiranmraine
closed
9 years ago
0