mgymrek/pybamview issues and pull requests

#52 - Possible Remote Code Execution Vulnerability

Issue - State: open - Opened by tch1bo almost 6 years ago

#51 - I have a problem using pybamview.

Issue - State: open - Opened by kds135 over 7 years ago - 2 comments

#50 - Small changes for Python 3 compatibility

Pull Request - State: open - Opened by bjoernpollex almost 8 years ago

#49 - check for both .bai and .bam.bai indices

Pull Request - State: closed - Opened by mgymrek over 8 years ago

#48 - Extremely high coverage loci

Issue - State: open - Opened by mgymrek over 8 years ago
Labels: bug

#47 - Replace pyfasta with pyfaidx

Pull Request - State: closed - Opened by mdshw5 almost 9 years ago - 3 comments

#46 - Extend error thrown when no samples in BAM file

Pull Request - State: closed - Opened by fomightez almost 9 years ago - 1 comment

#45 - snapbam: generate alignment views from the command line

Pull Request - State: closed - Opened by mgymrek almost 9 years ago

#44 - Look for index as either file.bai or file.bam.bai

Issue - State: closed - Opened by mgymrek about 9 years ago - 2 comments
Labels: bug

#43 - implementing option to downsample reads

Pull Request - State: closed - Opened by mgymrek over 9 years ago

#42 - Develop

Pull Request - State: closed - Opened by moonso over 9 years ago - 12 comments

#41 - Flask blueprint tweaks

Pull Request - State: closed - Opened by robinandeer over 9 years ago - 4 comments

#40 - paired-end

Issue - State: open - Opened by kspham over 9 years ago - 1 comment
Labels: enhancement

#39 - Use flask blueprint

Pull Request - State: closed - Opened by robinandeer almost 10 years ago - 2 comments

#38 - Flask app factory

Pull Request - State: closed - Opened by robinandeer almost 10 years ago - 2 comments

#37 - Look into using pyfaidx instead of pyfasta

Issue - State: closed - Opened by mgymrek almost 10 years ago - 1 comment

#36 - Use entry points

Pull Request - State: closed - Opened by robinandeer almost 10 years ago - 3 comments

#35 - On using Flask Blueprints

Issue - State: closed - Opened by robinandeer almost 10 years ago - 6 comments

#34 - add -100bp, -10bp, +10bp, +100bp nav buttons.

Pull Request - State: closed - Opened by andynu almost 10 years ago - 2 comments

#33 - Chromnames

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#32 - add option to only load a single bam file instead of whole directory

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#31 - removing pandas requirement

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#30 - Remove pandas dependency

Issue - State: closed - Opened by mgymrek about 10 years ago - 1 comment
Labels: enhancement

#29 - updating default location

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#28 - Read group strings

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#27 - Improve the default region first displayed

Issue - State: closed - Opened by laserson about 10 years ago - 3 comments

#26 - Support for Python 2.4+

Pull Request - State: closed - Opened by laserson about 10 years ago - 3 comments

#25 - "." in read groups breaks

Issue - State: closed - Opened by mgymrek about 10 years ago - 2 comments
Labels: bug

#24 - Add option to use a single specified bam rather than an entire directory

Issue - State: closed - Opened by mgymrek about 10 years ago - 1 comment
Labels: enhancement

#23 - Exper

Pull Request - State: closed - Opened by dlrice about 10 years ago - 3 comments

#22 - Version tags for 1.0.4 and 1.0.5

Issue - State: closed - Opened by jrandall about 10 years ago - 1 comment

#21 - fixing problem where read group is not a string

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#20 - fixing bug in text too big for zoom out 2x

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#19 - fixing snapshot bug

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#18 - Smallfixes

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#17 - D3

Pull Request - State: closed - Opened by mgymrek about 10 years ago

#16 - Handle fasta files with extra information in chromosome names

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment

#15 - Fail nicely with invalid BAM headers

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment

#14 - Load by sample

Pull Request - State: closed - Opened by mgymrek over 10 years ago

#13 - load by sample rather than by bam

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment

#12 - Export svg

Pull Request - State: closed - Opened by mgymrek over 10 years ago

#11 - Add support for annotating simple variants from an input VCF file

Issue - State: open - Opened by mgymrek over 10 years ago
Labels: enhancement

#10 - make sample headers scroll with alignments

Issue - State: closed - Opened by mgymrek over 10 years ago - 2 comments
Labels: bug

#9 - Add feature to render output as PDF

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment
Labels: enhancement

#8 - Target loci

Pull Request - State: closed - Opened by mgymrek over 10 years ago

#7 - ParseCigar for c in cigar: TypeError: 'NoneType' object is not iterable

Issue - State: closed - Opened by trickytank over 10 years ago - 2 comments

#6 - Allow multiple same-named read groups across BAMs

Pull Request - State: closed - Opened by ihaque over 10 years ago - 2 comments

#5 - highlight positions not matching the reference

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment
Labels: enhancement

#4 - add arrows for jumping navigation

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment

#3 - Handle all CIGAR cases.

Issue - State: closed - Opened by mgymrek over 10 years ago - 3 comments

#2 - Only works when installed using "sudo python setup.py install".

Issue - State: closed - Opened by mgymrek over 10 years ago - 2 comments
Labels: bug

#1 - Alignment scrolling jumps when scrolling past insertions

Issue - State: closed - Opened by mgymrek over 10 years ago - 1 comment

GitHub / mgymrek/pybamview issues and pull requests