pysam-developers pysam issues

pysam-developers / 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

764 stars 275 forks source link

issues

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No option to flush VariantFile.write() (or at least undocumented)

#1299 blex-max opened 5 days ago
1
[BUG][Typing] `PileupColumn` not imported in `libcalignmentfile.pyi`

#1298 vepain opened 6 days ago
0
iterating on unnamed streams

#1297 cmdoret opened 1 week ago
0
fix(libcalignmentfile.pyi): update IteratorColumn with missing import + correct _iter_ object

#1296 mshunjan opened 1 week ago
0
Improve cigarstring performance

#1295 limwz01 opened 3 weeks ago
0
Feature with cigar

#1294 DrYak opened 4 weeks ago
1
Feature skip softclip

#1293 DrYak opened 1 month ago
0
[Feature request] option to ignore soft-clipped parts in get_aligned_pairs()

#1292 LaraFuhrmann opened 1 month ago
5
Base modifications test failing

#1291 SoapGentoo closed 1 month ago
1
fetch gives wrong results on MD tag when read CRAM files with multiple_iterators=True

#1290 fanxinping opened 1 month ago
0
import samtools/bcftools/htslib 1.20

#1289 ilia-kats opened 2 months ago
0
Filter line always added to the VCF header when opening a file for writing

#1288 nh13 closed 2 months ago
0
Error running `bcftools plugin`

#1287 awgymer opened 2 months ago
5
Pysam on Azure ML

#1286 bounaux opened 2 months ago
0
CIRIquant: Error

#1285 atul2422 opened 2 months ago
0
Several tests fail: 2 failed, 155 errors

#1284 yurivict opened 2 months ago
1
about read.get_aligned_pairs(matches_only=True, with_seq=True)

#1283 bioinformatica opened 2 months ago
1
ModuleNotFoundError when using pysam in conda environment

#1282 ayushm64 closed 2 months ago
3
Speed up bcf genotype count

#1281 astaric opened 2 months ago
0
Accessing PL field is slow when number of samples gets large

#1280 astaric opened 2 months ago
0
Segmentation fault with very simple code

#1279 dbolser closed 2 months ago
4
Pysam .csi index support & how to deal with large references

#1278 RNieuwenhuis opened 3 months ago
0
Can't read files on s3

#1277 BenjaminSargsyan opened 3 months ago
0
Prebuilt wheels do not work on FIPS-compliant systems

#1276 shaze opened 3 months ago
4
+ document how to run bcftools commands from pysam

#1275 indraniel opened 3 months ago
0
MinGW version of pysam

#1274 teepean opened 3 months ago
3
fix: add missing properties to AlignedSegment type stubs

#1273 msto closed 2 months ago
2
Feature proposal: SAM tag enum

#1272 msto opened 4 months ago
1
import error

#1271 ssv1024 opened 4 months ago
0
Automatically translate VariantRecord on write

#1270 kkchau opened 4 months ago
1
Does not parse MM tag properly with when '.' ambiguity character is present

#1269 ddubocan closed 3 days ago
2
In pysam 0.22.0, AlignmentFile(REMOTE_BAM) reports SSL CA cert error with remote bam files

#1268 litaifang closed 2 months ago
2
Add AlignedSegment.__repr__

#1267 marcelm opened 5 months ago
0
AlignmentFile from String or StringIO support

#1266 MauroIb opened 5 months ago
0
variant type determination

#1265 arpanda opened 5 months ago
0
samfile.count()

#1264 AzureLii opened 5 months ago
0
ValueError: could not create iterator for region 'himom'

#1263 dbolser opened 6 months ago
1
ImportError ; libhts.so.2: cannot open shared object file: No such file or directory

#1262 poddarharsh15 opened 6 months ago
0
fix get_messages in docs

#1261 mbhall88 opened 6 months ago
0
set_encoding_error_handler example

#1260 nathanLauHKGI opened 6 months ago
0
How can I set the compression level of a BAM file when writing?

#1259 clintval opened 6 months ago
3
Allow accessing "END" as an info field to enable parsing of inter-chr SVs

#1258 jrobinso closed 6 months ago
2
Pysam returning libcurl error 77 when accessing public S3 file?

#1257 daisieh opened 6 months ago
6
pileup() in 0.22 is slower than 0.16.0.1

#1256 Crispy13 opened 7 months ago
0
CIGAR ops names in docs don't match the ones in the code

#1255 notestaff opened 7 months ago
0
Why is the site coverage of pileup different from that observed by igv？

#1254 haogecat opened 7 months ago
2
Fails to build with Python3.12

#1253 tillea closed 7 months ago
2
infer_query_length ignores soft-clipped (S) bases

#1252 Manuel-DominguezCBG closed 7 months ago
3
I want to use pysam to get the PS number in the vcf file

#1251 ZON-ZONG-MIN opened 7 months ago
1
htslib: Fix mmap configure check for current compilers

#1250 fweimer-rh closed 7 months ago
1