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Issues: pysam-developers/pysam

Python version survey
#1230 opened Oct 3, 2023 by jmarshall
Open 13
Build fails on Windows
#1320 opened Dec 12, 2024 by RPINerd
Open 2
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273 Open 659 Closed
273 Open 659 Closed
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Issues list

pysam.bcftools.concat Ignores the -o Option
#1323 opened Dec 19, 2024 by shokrofont
Unable to change type of FORMAT field despite updating header
#1321 opened Dec 12, 2024 by kjaisingh
Build fails on Windows
#1320 opened Dec 12, 2024 by RPINerd
2
query_alignment_length returns read length if read is unmapped / query_alignment_end returns end of read if unmapped
#1319 opened Dec 9, 2024 by schorlton-bugseq
aligned chromosomes of some reads are not displayed correctly in pysam
#1318 opened Nov 18, 2024 by creaturemoon
A bug seems to occur when editing contigs information of a vcf header.
#1314 opened Oct 21, 2024 by Dentalium
1
Request for information on VariantRecord instantiation
#1311 opened Oct 14, 2024 by blex-max
2
Confusing behaviour of VariantRecord.filter
#1309 opened Oct 1, 2024 by awgymer
Trying to add tags to an insilico AlignedSegment results in error
#1304 opened Aug 22, 2024 by blex-max
1
HTSlib warnings can't be suppressed?
#1303 opened Aug 14, 2024 by ohickl
Unmapped pairs with pileup
#1302 opened Jul 30, 2024 by ngaitan55
liblzma issue
#1301 opened Jul 29, 2024 by UniAlberta
Pysam ignoring some reads?
#1300 opened Jul 29, 2024 by rLannes
iterating on unnamed streams
#1297 opened Jul 9, 2024 by cmdoret
[Feature request] option to ignore soft-clipped parts in get_aligned_pairs()
#1292 opened Jun 6, 2024 by LaraFuhrmann
6
fetch gives wrong results on MD tag when read CRAM files with multiple_iterators=True
#1290 opened May 22, 2024 by fanxinping
Error running bcftools plugin
#1287 opened May 7, 2024 by awgymer
5
Pysam on Azure ML
#1286 opened May 3, 2024 by bounaux
CIRIquant: Error
#1285 opened Apr 29, 2024 by atul2422
about read.get_aligned_pairs(matches_only=True, with_seq=True)
#1283 opened Apr 24, 2024 by bioinformatica
1
Accessing PL field is slow when number of samples gets large
#1280 opened Apr 22, 2024 by astaric
Pysam .csi index support & how to deal with large references
#1278 opened Apr 10, 2024 by RNieuwenhuis
Can't read files on s3
#1277 opened Apr 5, 2024 by BenjaminSargsyan
Prebuilt wheels do not work on FIPS-compliant systems
#1276 opened Apr 3, 2024 by shaze
4
Feature proposal: SAM tag enum
#1272 opened Mar 15, 2024 by msto
1
ProTip! What’s not been updated in a month: updated:<2024-11-24.