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pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
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Fix multiarch macOS build by removing brewed liblzma
#1207
jmarshall
closed
1 year ago
0
Can't install via conda on Apple Silicon macOS
#1206
koh2ng0
closed
2 months ago
2
pysam build fails for python 3.11 + macOS 12.6.7
#1205
tedil
closed
1 year ago
1
ValueError: I/O operation on closed file when reading .vcf file and get samples
#1204
cpwater
opened
1 year ago
2
Error about temporary directory
#1203
quliping
closed
1 year ago
1
Can't install via conda for Python 3.11
#1202
Shruteek
closed
1 year ago
3
Update handling of INFO/END when writing records in VCF
#1201
rickymagner
opened
1 year ago
2
[VCFs] Modifying END position works for insertions but not deletions
#1200
rickymagner
opened
1 year ago
1
Is the issue"subprocess-exited-with-error" fixed?
#1199
AlenGhzau
opened
1 year ago
2
samtools/*.c: fix a couple of typos.
#1198
emollier
closed
1 year ago
2
in pileup, discrepancy between stepper all and stepper samtools reads
#1197
Pagey
closed
1 year ago
1
When SAM line query_qualities="*"; AlignedSegment query_qualities -> Long incorrect array
#1196
dvklopfenstein
closed
1 year ago
1
pysam.fastq: OSError: [Errno 9] Bad file descriptor
#1195
schorlton
opened
1 year ago
0
Remove cython runtime dependency from pyproject.toml
#1194
aryarm
closed
1 year ago
1
pysam.mpileup(*cmd, catch_stdout=False) does not write to stdout
#1193
biermanr
opened
1 year ago
0
PySAM installation on macbook Pro M2
#1192
Taslimi
closed
10 months ago
2
Issue installing pysam from bioconda with python 3.11
#1191
fgvieira
closed
1 year ago
1
pysam requires openssl 1.1.1t-1.1.2a but that is ancient
#1190
aldertzomer
closed
1 year ago
1
Improve type hints for AlignmentFile iteration
#1189
jmarshall
closed
1 year ago
0
Fix AlignmentFile iteration type hints by adding AlignmentFileIterator class
#1188
jmarshall
closed
1 year ago
2
Record Order with fetch
#1187
mattjvincent
opened
1 year ago
0
Remove cython from runtime dependencies
#1186
nsoranzo
closed
1 year ago
2
HTSFile.seek(whence)
#1185
ylluX
closed
1 year ago
0
Iterating over AlignmentFile not properly type-hinted
#1184
PikalaxALT
closed
1 year ago
1
fix-cybuildwheel-version
#1183
AndreasHeger
closed
1 year ago
0
0.21 pypi release
#1182
tfwillems
closed
1 year ago
0
OSError: [Errno 22] b'Invalid argument' in writing the VCF
#1181
masterzhen119
opened
1 year ago
0
get_reference_sequence with_seq=True returns different reference for same position?
#1180
semenko
closed
1 year ago
5
Failures on Cython 3
#1179
SoapGentoo
closed
1 year ago
8
updated release notes
#1178
AndreasHeger
closed
1 year ago
5
V0.21.0
#1177
AndreasHeger
closed
1 year ago
3
Install from github: failed to set dynamic section sizes: bad value
#1176
Hrovatin
closed
1 year ago
8
[W::bcf_update_info] INFO/END=0 is smaller than POS at chr1:1
#1175
arpanda
closed
1 year ago
1
can't install with python 3.11
#1174
benjschiller
closed
1 year ago
2
Fix building htscodecs SIMD code on multi-arch macOS
#1173
jmarshall
closed
1 year ago
2
Update imports to htslib/samtools/bcftools 1.17
#1172
jmarshall
closed
1 year ago
1
Remove py3.6 from ci
#1171
AndreasHeger
closed
1 year ago
0
Renaming Chromosomes in vcf/bcf files
#1170
Lewis-W-S-Fisher
opened
1 year ago
1
Test failures on musl with python 3.10
#1169
SoapGentoo
closed
1 year ago
2
Add a minimal pyproject.toml for PEP517
#1168
afg1
closed
1 year ago
2
pysam vcf record
#1167
tanyasarkjain
closed
1 year ago
3
ValueError: reference sequence for 'b'2'' (tid=1) not found
#1166
lwtan90
opened
1 year ago
4
Memory leak when fetching from CRAM files
#1165
anh151
opened
1 year ago
2
[Quesion] AlignedSegment unique ID
#1164
spaceben
closed
1 year ago
1
get_query_sequences function from pileupcolumn class fails to display in samtools mpileup format
#1163
lstbl
opened
1 year ago
1
Header ALT to a record
#1162
arpanda
opened
1 year ago
0
Sequencing depth differ on a coordinate, based on surrounding genomic range input.
#1161
codemeleon
opened
1 year ago
4
Initialize FastaFile Object from Sequence
#1160
lwtan90
opened
1 year ago
0
is FastaFile object thread-safe?
#1159
lwtan90
opened
1 year ago
0
Fix type hint for IteratorRow's __next__
#1158
tfwillems
closed
1 year ago
1
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