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Feature Request: Name-based read fetching for FASTQ

Status: Open.

#1408 In pysam-developers/pysam;

· samarendra-pani opened on May 4, 2026

Inconsistent behavior of rec.start, rec.stop and rec.rlen in 0.24

Status: Open.

#1407 In pysam-developers/pysam;

· ilyasoifer opened on Apr 29, 2026

-o not work for pysam.bcftools.norm

Status: Open.

#1397 In pysam-developers/pysam;

· PlatonB opened on Mar 19, 2026

Samtools instructions like pysam.view() and pysam.sort() continue forever with empty inputs and cannot be interrupted.

Status: Open.

#1395 In pysam-developers/pysam;

· timslittle opened on Mar 11, 2026

Feature Request: Add option to omit UR field in CRAM headers

Status: Open.

#1378 In pysam-developers/pysam;

· fplazaonate opened on Feb 11, 2026

pileup reloads BAI index

Status: Open.

#1377 In pysam-developers/pysam;

· suhrig opened on Feb 9, 2026

libcbcf classes should implement Python3-style dict methods rather than Python2-style

Status: Open.

#1373 In pysam-developers/pysam;

· jmarshall opened on Jan 6, 2026

Using pysam as an interface to in-memory bam1_t objects

Status: Open.

#1369 In pysam-developers/pysam;

· blex-max opened on Nov 25, 2025

API for parsing MM&ML tags

Status: Open.

#1357 In pysam-developers/pysam;

· Ming-Lian opened on Sep 5, 2025

Get query sequences in a gap region

Status: Open.

#1356 In pysam-developers/pysam;

· ericgonzalezs opened on Aug 25, 2025

Create an iterator over PileupColumns from a list of AlignedSegments

Status: Open.

#1352 In pysam-developers/pysam;

· nh13 opened on Jul 3, 2025

Feature Request: Faster Single-Base Access for Long Reads

Status: Open.

#1346 In pysam-developers/pysam;

· Crispy13 opened on Jun 7, 2025