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Issues: pysam-developers/pysam

Python version survey
#1230 opened Oct 3, 2023 by jmarshall
Open 8
Can't install via conda on Apple Silicon macOS
#1206 opened Jul 26, 2023 by koh2ng0
Open 1
Can't install via conda for Python 3.11
#1202 by Shruteek was closed Jun 30, 2023
Closed 2
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Issues list

CIRIquant: Error
#1285 opened Apr 29, 2024 by atul2422
Several tests fail: 2 failed, 155 errors
#1284 opened Apr 25, 2024 by yurivict
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
import error
#1271 opened Feb 28, 2024 by ssv1024
Does not parse MM tag properly with when '.' ambiguity character is present
#1269 opened Feb 23, 2024 by ddubocan
In pysam 0.22.0, AlignmentFile(REMOTE_BAM) reports SSL CA cert error with remote bam files
#1268 opened Feb 21, 2024 by litaifang
AlignmentFile from String or StringIO support
#1266 opened Feb 9, 2024 by MauroIb
variant type determination
#1265 opened Jan 30, 2024 by arpanda
samfile.count()
#1264 opened Jan 30, 2024 by AzureLii
ValueError: could not create iterator for region 'himom'
#1263 opened Jan 18, 2024 by dbolser
1
ImportError ; libhts.so.2: cannot open shared object file: No such file or directory
#1262 opened Jan 15, 2024 by poddarharsh15
set_encoding_error_handler example
#1260 opened Jan 4, 2024 by nathanLauHKGI
How can I set the compression level of a BAM file when writing?
#1259 opened Dec 26, 2023 by clintval
3
Pysam returning libcurl error 77 when accessing public S3 file?
#1257 opened Dec 20, 2023 by daisieh
2
pileup() in 0.22 is slower than 0.16.0.1
#1256 opened Dec 17, 2023 by Crispy13
CIGAR ops names in docs don't match the ones in the code
#1255 opened Dec 14, 2023 by notestaff
Why is the site coverage of pileup different from that observed by igv？
#1254 opened Dec 12, 2023 by haogecat
2
I want to use pysam to get the PS number in the vcf file
#1251 opened Dec 3, 2023 by ZON-ZONG-MIN
1
Pysam.TabixFile not recognising S3 URL
#1249 opened Nov 30, 2023 by Mathew-B-SDGS
1
PileupColumn.get_query_positions() behavior differs from PileupRead.query_position
#1248 opened Nov 30, 2023 by jkoubele
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