Issues

• Segmentation fault in sambamba depth base

  bug
  biod/sambamba#522 · Filter by author emollier opened on Feb 7, 2025

• Link in Github repo top right corner goes 404: https://thebird.nl/blog/D_Dragon.html

  bug
  biod/sambamba#521 · Filter by author corneliusroemer opened on Dec 3, 2024

• A Segmentation fault occurred in the sambamba markdup

  bug
  biod/sambamba#520 · Filter by author Xiangyue-Meng opened on Aug 20, 2024

• sambamba markdup stuck in the finding positions of the duplicate reads in the file...

  biod/sambamba#519 · Filter by author xiechangxiao opened on Jul 11, 2024

• sambamba (v. 0.8.0) sort: exit code 271

  bug
  biod/sambamba#517 · Filter by author jeffreycyyu opened on May 14, 2024

• sambamba-sort: index [1] exceeds array of length 1

  bug
  biod/sambamba#516 · Filter by author timholyy opened on Apr 18, 2024

• Sambamba slice - 94 Segmentation fault (core dumped)

  bug
  biod/sambamba#515 · Filter by author alexvasilikop opened on Feb 5, 2024
  2

• mpileup fail to execute bin/sh

  bug
  biod/sambamba#514 · Filter by author ghost opened on Nov 23, 2023

• sambamba slice piped with sambamba view is having runtime problem when running in parallel

  bug
  biod/sambamba#513 · Filter by author yangyxt opened on Oct 22, 2023

• problem of deduplication

  bug
  biod/sambamba#512 · Filter by author crazysummerW opened on Sep 20, 2023

• Support removal of duplicates for paired-end reads

  bug
  biod/sambamba#511 · Filter by author rikrdo89 opened on Sep 14, 2023

• Difference of depth/mean coverage calculation among sambamba, bedtools, and mosdepth in high coverage panel data

  biod/sambamba#510 · Filter by author ipstone opened on Sep 13, 2023

• sambamba-markdup：(No space left on device)

  biod/sambamba#509 · Filter by author weirdo-onlooker opened on Sep 6, 2023
  1

• Sambamba subsample produces truncated BAMs

  bug
  biod/sambamba#506 · Filter by author Sven-Winter opened on Jun 14, 2023

• Sambamba depth output repeats positions!

  bug
  biod/sambamba#505 · Filter by author Sven-Winter opened on May 30, 2023

• sambamba-markdup: Range violation

  bug
  biod/sambamba#501 · Filter by author Cynthia1012 opened on Feb 16, 2023
  2

• Can you add sort by tag function?

  Follow the checklist to report an issue
  biod/sambamba#499 · Filter by author cherryamme opened on Dec 13, 2022
  1

• extends past source array of length 131072

  bug
  biod/sambamba#498 · Filter by author charliechen912ilovbash opened on Dec 9, 2022

• sambamba depth region: Segmentation fault (core dumped)

  Follow the checklist to report an issuesupport request - please use google groups instead
  biod/sambamba#492 · Filter by author QichenFU opened on Jul 13, 2022

• depth region -L for multiple bam

  biod/sambamba#491 · Filter by author yuanjianwen-gif opened on Jun 10, 2022

• Feature request: fixmate like samtools

  enhancementhelp wanted
  biod/sambamba#489 · Filter by author kaji331 opened on May 24, 2022
  1

• Feature request: Slice BAM file by query name

  enhancementhelp wanted
  biod/sambamba#488 · Filter by author yangyxt opened on May 9, 2022
  1

• can sambamba markdup give duprate concrete number?

  bug
  biod/sambamba#487 · Filter by author asmlgkj opened on Apr 27, 2022

• sambamba --version's output doubled

  bug
  biod/sambamba#486 · Filter by author kim-fehl opened on Mar 28, 2022
  1

• Samtools + libdeflate out performs sambamba on a single thread

  enhancement
  biod/sambamba#485 · Filter by author mebbert opened on Feb 26, 2022
  3