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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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Why is the site coverage of pileup different from that observed by igv?
#1254
haogecat
opened
8 months ago
2
Fails to build with Python3.12
#1253
tillea
closed
8 months ago
2
infer_query_length ignores soft-clipped (S) bases
#1252
Manuel-DominguezCBG
closed
8 months ago
3
I want to use pysam to get the PS number in the vcf file
#1251
ZON-ZONG-MIN
opened
8 months ago
1
htslib: Fix mmap configure check for current compilers
#1250
fweimer-rh
closed
8 months ago
1
Pysam.TabixFile not recognising S3 URL
#1249
Mathew-B-SDGS
opened
9 months ago
1
PileupColumn.get_query_positions() behavior differs from PileupRead.query_position
#1248
jkoubele
opened
9 months ago
0
Add ``htslib/hts_probe_cc.sh`` to sdist
#1247
nsoranzo
closed
4 months ago
2
pysam.FastaFile reverse-complement function?
#1246
jgrg
opened
9 months ago
0
Add FastxRecord to the docs
#1245
nh13
opened
9 months ago
1
Seeking assistance
#1244
liujilei156231
closed
9 months ago
1
Test for equality of FastxRecord
#1243
clintval
opened
9 months ago
3
Cython version requirements (are varying for different Python releases)
#1242
tillea
opened
9 months ago
3
running samtools view command produces no output
#1241
robertwhbaldwin
opened
10 months ago
1
reconsituted AlignedSegment is not equivalent to original
#1240
tzuni
opened
10 months ago
1
Failed to build pysam wheel, throws Cython error.
#1239
jsquaredosquared
closed
10 months ago
0
Add missing SQ tags as per the spec
#1238
nh13
closed
10 months ago
2
AlignmentHeader.from_dict() silently discards the TP attribute from SQ lines
#1237
tfenne
opened
10 months ago
3
from pysam.libchtslib import * ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
#1236
npont
opened
10 months ago
0
Fix error text when array tag typecode is invalid
#1235
marcus1487
opened
10 months ago
5
Use relative cimports rather than luck
#1234
jmarshall
closed
10 months ago
0
AttributeError: module 'array' has no attribute 'typecode'
#1233
weishwu
opened
10 months ago
0
POS 0 cannot be written
#1232
awgymer
opened
10 months ago
1
Our make-based libhts.a build produces incorrect results when cross-compiling
#1231
jmarshall
opened
10 months ago
0
Python version survey
#1230
jmarshall
opened
10 months ago
8
Support "--reverse-del" option of pileup in pysam?
#1229
y9c
opened
11 months ago
0
squigualiser reform: object of type 'NoneType' has no len()
#1228
Marjan-Hosseini
closed
11 months ago
1
fix: improve parsing performance
#1227
valentynbez
closed
11 months ago
1
Segmentation fault when calling `get_aligned_pairs(with_seq = True)`
#1226
isaacvock
closed
11 months ago
3
TypeError: values expected to be 3-tuple, given len=2 even for haploid GT values
#1225
karinkumar
opened
11 months ago
1
Error when I install my pysam!
#1224
Neo-xbx-00
opened
11 months ago
2
Is there a way to sort VCF/BCF, like pysam.sort?
#1223
antonylebechec
closed
11 months ago
2
InError: Invalid BCF, the FORMAT tag id=91 at chr20:60137 not present in the header
#1222
karinkumar
closed
11 months ago
2
Relaxing Python version requirement in Bioconda?
#1221
cmeesters
closed
11 months ago
1
Adding contig tag to a output vcf file header shifting chrom numbers in records
#1220
nathanLauHKGI
opened
11 months ago
1
Remove `requires` from `setup()` etc (combines 1216 & 1218)
#1219
jmarshall
closed
11 months ago
1
Pin cython<4
#1218
ahvigil
closed
11 months ago
2
more stringent cython version pin
#1217
ahvigil
closed
11 months ago
2
Move Cython to build dependencies in `setup.py`
#1216
althonos
closed
11 months ago
4
pysam.fetch on S3 Bucket
#1215
StephanHolgerD
closed
11 months ago
5
handle expected [E::idx_find_and_load] without stopping execution
#1214
sroener
closed
12 months ago
5
Prepare for Python 3.12 by avoiding distutils in setup.py
#1213
jmarshall
closed
12 months ago
1
Add HTSFile.seek(..., whence) parameter & clarify libc. vs io.SEEK_SET
#1212
jmarshall
closed
1 year ago
0
pysam crashes when quality only has a single value of "*"
#1211
ymcki
opened
1 year ago
2
Potential Bug: Miss Assigned Contig name for variants by VariantFile
#1210
gudeqing
opened
1 year ago
0
pysam consensus options
#1209
noamprywes
closed
1 year ago
3
Update imports to htslib/samtools/bcftools 1.18
#1208
jmarshall
closed
12 months ago
0
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
1 month ago
2
pysam build fails for python 3.11 + macOS 12.6.7
#1205
tedil
closed
1 year ago
1
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