Ensembl Bio-DB-HTS issues

Ensembl / Bio-DB-HTS

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib

Apache License 2.0

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issues

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Archives install script tied to master

#59 avullo closed 6 years ago
3
Allows BAM with csi index to be used

#58 keiranmraine closed 6 years ago
0
Does not support csi index

#57 keiranmraine closed 6 years ago
9
Calling coverage on a BAM re-fetches the header every time

#56 ah19 opened 6 years ago
4
BCF indexing

#55 rishidev closed 6 years ago
3
'missing SAM header' when opening SAM files

#54 AlexanderDilthey closed 6 years ago
1
Changes in preperation for v2.8 release

#53 rishidev closed 7 years ago
0
HTSlib v1.5 default

#52 rishidev closed 7 years ago
0
Update Travis CI test Perl version to 5.26

#51 rishidev closed 7 years ago
0
Add DESTROY methods for guaranteed resources dealloction

#50 Zhicheng-Liu closed 7 years ago
0
use filetest 'access'; to allow POSIX ACLs

#49 CanWood closed 7 years ago
0
Update HTS.pm

#48 CanWood closed 7 years ago
1
Changes to use HTSlib hisremote function

#47 rishidev closed 7 years ago
0
Switch to using hisremote

#46 andrewyatz closed 7 years ago
1
Add output filename to wget command

#45 Zhicheng-Liu closed 7 years ago
1
The install script fails with GNU Wget 1.12

#44 dbolser-ebi closed 7 years ago
4
One minor improvement and one minor bugfix

#43 dbolser-ebi closed 7 years ago
2
Adding lzma, libbz2 and curl dev libs

#42 andrewyatz closed 7 years ago
1
Treat s3:// urls as remote as htslib 1.3 onwards supports it

#41 ah19 closed 7 years ago
7
padded_alignment() produces invalid output

#40 AlexanderDilthey opened 7 years ago
27
BufferOverflow error

#39 ghost closed 7 years ago
3
Specify correct end when calling coverage if none specified

#38 rishidev closed 8 years ago
0
Coverage from Cram input

#37 ghost closed 8 years ago
4
Create a way to Tabix query against chr containing ':'

#36 keiranmraine closed 8 years ago
2
Impelement write capability

#35 riederd closed 8 years ago
3
* Implemented initial BAM writing capabilities

#34 riederd closed 8 years ago
1
Error while installing VEP

#33 raonyguimaraes closed 8 years ago
2
Ancillary items from Bio-SamTools

#32 ghost closed 8 years ago
5
Why didn't you just rename the repo?

#31 keiranmraine closed 8 years ago
2
Split HTSLIB_DIR into HTSLIB_LIBDIR and HTSLIB_INCDIR

#30 mmokrejs closed 7 years ago
7
Build failure under Fedora 23

#29 biogberg closed 8 years ago
8
Does Bio-HTS use ENA for CRAM tests?

#28 andrewyatz closed 8 years ago
16
system exit codes not checked - silent install failures

#27 keiranmraine closed 8 years ago
2
feat(remote file): enable https support for remote access

#26 Zhicheng-Liu closed 8 years ago
1
Feature/bcf2016

#25 rishidev closed 8 years ago
1
Adding first pass implementation of kseq from cjfields

#24 andrewyatz closed 8 years ago
1
Use reftype() not ref() to find the underlying structure a ref points at

#23 andrewyatz closed 8 years ago
1
Bugfix/free str with no return

#22 andrewyatz closed 8 years ago
0
free str in tabix header

#21 rishidev closed 8 years ago
0
Adding DESTROY back in with a HASH ref check

#20 andrewyatz closed 8 years ago
2
Bugfix/tabix destroy hash

#19 rishidev closed 8 years ago
7
Make sure to free the string

#18 andrewyatz closed 8 years ago
6
Memory leak: Bio::DB::HTS::Tabix - very reproducible

#17 keiranmraine closed 8 years ago
20
use depth and master branch when cloning in INSTALL.pl

#16 rishidev closed 8 years ago
0
INSTALL.pl - use master.zip instead of git clone

#15 keiranmraine closed 8 years ago
20
Functionality to write bam file

#14 sb43 closed 8 years ago
3
Bio::DB::HTS::Tabix - docs not accurate

#13 keiranmraine closed 8 years ago
1
Release/v1.12 for CPAN

#12 rishidev closed 8 years ago
0
Add TravisCI testing

#11 rishidev closed 8 years ago
0
Trivial fix to pod

#10 keiranmraine closed 8 years ago
1

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