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pysam
Automatically exported from code.google.com/p/pysam
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Problems using pysam in combination with python-pp
#105
GoogleCodeExporter
closed
9 years ago
1
Opening a SAM or BAM file without SQ fields in the header
#104
GoogleCodeExporter
closed
9 years ago
1
Doesn't compile on OS X 10.8 (or clang)
#103
GoogleCodeExporter
closed
9 years ago
2
RPKM_count.py doesn't work with new pysam libraries
#102
GoogleCodeExporter
closed
9 years ago
2
Integer tag gets changed after using pysam
#101
GoogleCodeExporter
closed
9 years ago
1
NotImplementedError: tags field too large
#100
GoogleCodeExporter
closed
9 years ago
1
Segmentation fault when accessing aligned read in pileup column
#99
GoogleCodeExporter
closed
9 years ago
2
pysam index does not work in ipython / during automated tests
#98
GoogleCodeExporter
closed
9 years ago
3
CIGAR String Does not accept tuples of length 1
#97
GoogleCodeExporter
closed
9 years ago
2
Allow custom headers in Samfile
#96
GoogleCodeExporter
closed
9 years ago
1
.fetch and .count different from samtools view
#95
GoogleCodeExporter
closed
9 years ago
3
Documentation request.
#94
GoogleCodeExporter
closed
9 years ago
1
pysam pileup max_depth > 8000
#93
GoogleCodeExporter
closed
9 years ago
2
Error in updating read.tags
#92
GoogleCodeExporter
closed
9 years ago
4
Quadratic behaviour in header generation
#91
GoogleCodeExporter
closed
9 years ago
1
pysam.SamtoolsError
#90
GoogleCodeExporter
closed
9 years ago
1
open: No such file or directory
#89
GoogleCodeExporter
closed
9 years ago
1
Python 3 support
#88
GoogleCodeExporter
closed
9 years ago
1
Improve read.positions to report (read base, ref base)
#87
GoogleCodeExporter
closed
9 years ago
2
Memory Leak In IteratorRowRegion
#86
GoogleCodeExporter
closed
9 years ago
1
Pysam doesn't support VCF 4.1 yet?
#85
GoogleCodeExporter
closed
9 years ago
3
Headers are not always correctly parsed
#84
GoogleCodeExporter
closed
9 years ago
7
Expose More Of The Cython Interface
#83
GoogleCodeExporter
closed
9 years ago
1
Pysam adding support for FO and KS header fields
#82
GoogleCodeExporter
closed
9 years ago
3
Support for FZ (flow intensities) field with B (array) of small ints
#81
GoogleCodeExporter
closed
9 years ago
3
Creating a BAM from referencenames and referencelengths does not add a text header with SQ
#80
GoogleCodeExporter
closed
9 years ago
2
Negative integer-valued tag
#79
GoogleCodeExporter
closed
9 years ago
3
output BAM does not have EOF marker
#78
GoogleCodeExporter
closed
9 years ago
3
End points in Python should be 1-based
#77
GoogleCodeExporter
closed
9 years ago
2
pysam AlignedRead properties reflect old names in SAM specification
#76
GoogleCodeExporter
closed
9 years ago
3
str(AlignedRead) does not format RNEXT aka MRNM correctly (SAM column 6)
#75
GoogleCodeExporter
closed
9 years ago
4
str(AlignedRead) does not format SAM tags correctly
#74
GoogleCodeExporter
closed
9 years ago
1
pysam.Samfile(sam_filename) won't work without SAM headers
#73
GoogleCodeExporter
closed
9 years ago
3
pysam.Samfile(sam_filename, "rU")) not allowed
#72
GoogleCodeExporter
closed
9 years ago
1
Float tags prevent opt() from finding later tags (KeyError instead of value of present tag)
#71
GoogleCodeExporter
closed
9 years ago
3
Tags should return empty list instead of None if no tags are defined
#70
GoogleCodeExporter
closed
9 years ago
4
Expose pilup max depth setter
#69
GoogleCodeExporter
closed
9 years ago
3
Negative size passed to PyString_FromStringAndSize from IndelCall.second_allele
#68
GoogleCodeExporter
closed
9 years ago
1
close tabix file
#67
GoogleCodeExporter
closed
9 years ago
1
wrong info in documentation
#66
GoogleCodeExporter
closed
9 years ago
1
Samfile does not write header to SAM output when template or header kwargs supplied
#65
GoogleCodeExporter
closed
9 years ago
1
Read.rname returns integer not reference sequence name
#64
GoogleCodeExporter
closed
9 years ago
1
Pysam pileup limited to 8000 reads
#63
GoogleCodeExporter
closed
9 years ago
2
Trouble installing pysam (gcc-related error)
#62
GoogleCodeExporter
closed
9 years ago
1
Suggestion: accept lowercase header tags.
#61
GoogleCodeExporter
closed
9 years ago
2
pileup wrong range
#60
GoogleCodeExporter
closed
9 years ago
7
Can't compile with older cython?
#59
GoogleCodeExporter
closed
9 years ago
1
Samfile._filename is apperantly not freed on dealloc
#58
GoogleCodeExporter
closed
9 years ago
1
Read header of new bwa output fails
#57
GoogleCodeExporter
closed
9 years ago
3
pysam on PIP does not install
#56
GoogleCodeExporter
closed
9 years ago
4
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