vd4mmind pysam issues - Githubissues

vd4mmind / pysam

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unable to find file vcvarsall.bat

#155 GoogleCodeExporter opened 8 years ago
0
language_level is not set in the .pxd files

#154 GoogleCodeExporter opened 8 years ago
0
get_libraries() returns wrong library extension

#153 GoogleCodeExporter opened 8 years ago
0
Wrong .bai file => segmentation fault

#152 GoogleCodeExporter opened 8 years ago
1
pip3 install pysam fails if old cython installed

#151 GoogleCodeExporter opened 8 years ago
0
Pysam does not compile (Cython error)

#150 GoogleCodeExporter closed 8 years ago
1
Install fails on Mac OSX10.9 (Mavericks)

#149 GoogleCodeExporter opened 8 years ago
3
Removing distribute breaks Python 3 support

#148 GoogleCodeExporter closed 8 years ago
3
Does not allow DS field in PG record

#147 GoogleCodeExporter closed 8 years ago
1
Add AlignedRead.addTags for speed improvement

#146 GoogleCodeExporter closed 8 years ago
4
BAM open fails when index file is fname.bai instead of fname.bam.bai

#145 GoogleCodeExporter closed 8 years ago
1
Invalid header generation

#144 GoogleCodeExporter closed 8 years ago
1
parser parameter should be moved from Tabixfile.fetch to Tabixfile.__init__

#143 GoogleCodeExporter closed 8 years ago
2
Tabixfile.fetch() should accept a function as a parser

#142 GoogleCodeExporter closed 8 years ago
2
Tabixfile.fetch() should raise more specialized exception when a region can not be found in tabix file

#141 GoogleCodeExporter closed 8 years ago
2
Permissions in tarball

#140 GoogleCodeExporter closed 8 years ago
1
Symbol not found: ___sync_fetch_and_add

#139 GoogleCodeExporter closed 8 years ago
2
.c files should be distributed with source, Cython should not be required for install, and other build issues

#138 GoogleCodeExporter closed 8 years ago
6
BAM to Bio.SeqRecord (with quality)

#137 GoogleCodeExporter closed 8 years ago
4
Trying to call SNPs

#136 GoogleCodeExporter closed 8 years ago
1
editing reads in place

#135 GoogleCodeExporter closed 8 years ago
1
Doesn't find index files that end only in .bai

#134 GoogleCodeExporter closed 8 years ago
3
Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file.

#133 GoogleCodeExporter closed 8 years ago
3
truncated read groups

#132 GoogleCodeExporter closed 8 years ago
2
Segmentation fault on pysam.Samfile().pileup().next()

#131 GoogleCodeExporter closed 8 years ago
1
_samtools_dispatch() does not clean up tempfiles properly

#130 GoogleCodeExporter closed 8 years ago
1
garbage characters when changing tags

#129 GoogleCodeExporter closed 8 years ago
5
Tabix file fetch for region does not work for large coordinate values

#128 GoogleCodeExporter closed 8 years ago
3
"ValueError: level must be >= 0" when doing "import pysam" on Python 3

#127 GoogleCodeExporter closed 8 years ago
3
pysam installation under cygwin

#126 GoogleCodeExporter closed 8 years ago
1
until_eof parameter not exist

#125 GoogleCodeExporter closed 8 years ago
3
Executing git-cola is unsuccessful

#124 GoogleCodeExporter closed 8 years ago
1
installation assumes already installed?

#123 GoogleCodeExporter closed 8 years ago
7
Error loading 0.7.4 "Symbol not found: _getline"

#122 GoogleCodeExporter closed 8 years ago
10
pileup() seems broken.

#121 GoogleCodeExporter closed 8 years ago
2
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#120 GoogleCodeExporter closed 8 years ago
0
Import problem pysam eclipse (windows)

#119 GoogleCodeExporter closed 8 years ago
1
Fetching alignments from BAM files with a large number of reference sequences is prohibitively slow

#118 GoogleCodeExporter closed 8 years ago
2
Using pysam with an unaligned bam file

#117 GoogleCodeExporter closed 8 years ago
2
Pysam does not allow index without ".bam" component.

#116 GoogleCodeExporter closed 8 years ago
3
adding read group fails on longer sam records

#115 GoogleCodeExporter closed 8 years ago
2
problem with cigarstring attribute

#114 GoogleCodeExporter closed 8 years ago
2
Samfile.header fails with internal error on specific file

#113 GoogleCodeExporter closed 8 years ago
1
Typo in setup.pu

#112 GoogleCodeExporter closed 8 years ago
1
No error is raised when file system quota is reached.

#111 GoogleCodeExporter closed 8 years ago
1
Error reading Header for bam files with "PP" field code in record PG found in 1000 genome bam files

#110 GoogleCodeExporter opened 8 years ago
3
pysam.calmd output redirection

#109 GoogleCodeExporter closed 8 years ago
3
Not all 1.4 fields are known to pysam

#108 GoogleCodeExporter closed 8 years ago
1
truncate option in Samfile.pileup doesn't work

#107 GoogleCodeExporter closed 8 years ago
4
A bug in tabix_compress

#106 GoogleCodeExporter closed 8 years ago
1