Ecosyste.ms: Issues

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GitHub / biod/sambamba issues and pull requests

#520 - A Segmentation fault occurred in the sambamba markdup

Issue - State: open - Opened by Xiangyue-Meng 3 months ago
Labels: bug

#518 - Compile binary with ldc 1.38.0

Pull Request - State: open - Opened by corneliusroemer 5 months ago

#517 - sambamba (v. 0.8.0) sort: exit code 271

Issue - State: open - Opened by jeffreycyyu 6 months ago
Labels: bug

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

Issue - State: open - Opened by Bio-Quest 7 months ago
Labels: bug

#515 - Sambamba slice - 94 Segmentation fault (core dumped)

Issue - State: open - Opened by alexvasilikop 10 months ago - 2 comments
Labels: bug

#512 - problem of deduplication

Issue - State: open - Opened by crazysummerW about 1 year ago
Labels: bug

#511 - Support removal of duplicates for paired-end reads

Issue - State: open - Opened by rikrdo89 about 1 year ago
Labels: bug

#509 - sambamba-markdup：(No space left on device)

Issue - State: open - Opened by weirdo-onlooker about 1 year ago - 1 comment

#508 - chore: remove travis config

Pull Request - State: closed - Opened by chenrui333 about 1 year ago - 1 comment

#507 - sambamba 1.0.1 build failure

Issue - State: closed - Opened by chenrui333 over 1 year ago - 4 comments

#506 - Sambamba subsample produces truncated BAMs

Issue - State: open - Opened by Sven-Winter over 1 year ago
Labels: bug

#505 - Sambamba depth output repeats positions!

Issue - State: open - Opened by Sven-Winter over 1 year ago
Labels: bug

#504 - provide an example of pipping sambamba in documentation

Issue - State: closed - Opened by DrRLS over 1 year ago - 1 comment

#503 - conda sambamba 1.0 is running slower than conda sambamba 0.6

Issue - State: closed - Opened by ericpanyc over 1 year ago - 1 comment
Labels: bug

#502 - porting from old sambamba/BioD

Issue - State: closed - Opened by RichardCorbett over 1 year ago - 1 comment

#501 - sambamba-markdup: Range violation

Issue - State: open - Opened by Cynthia1012 almost 2 years ago - 2 comments
Labels: bug

#500 - Minor subversion number missing in 1.0 release

Issue - State: closed - Opened by Stikus almost 2 years ago - 3 comments
Labels: bug

#499 - Can you add sort by tag function?

Issue - State: open - Opened by cherryamme almost 2 years ago - 1 comment
Labels: Follow the checklist to report an issue

#498 - extends past source array of length 131072

Issue - State: open - Opened by charliechen912ilovbash almost 2 years ago
Labels: bug

#497 - Test suite error on Debian unstable

Issue - State: closed - Opened by tillea almost 2 years ago - 4 comments
Labels: bug

#496 - Add CI config for Github Actions

Pull Request - State: closed - Opened by martin-g about 2 years ago - 2 comments

#495 - Updates readme grammar, spelling, markdown

Pull Request - State: closed - Opened by nikoandpiko about 2 years ago - 1 comment

#494 - sambamba depth region function add median value

Issue - State: closed - Opened by tamadezhenshiyuncai about 2 years ago - 1 comment

#493 - Fixed a typo

Pull Request - State: closed - Opened by samsonjm over 2 years ago

#492 - sambamba depth region: Segmentation fault (core dumped)

Issue - State: open - Opened by QichenFU over 2 years ago
Labels: support request - please use google groups instead, Follow the checklist to report an issue

#491 - depth region -L for multiple bam

Issue - State: open - Opened by yuanjianwen-gif over 2 years ago

#489 - Feature request: fixmate like samtools

Issue - State: open - Opened by kaji331 over 2 years ago - 1 comment
Labels: enhancement, help wanted

#488 - Feature request: Slice BAM file by query name

Issue - State: open - Opened by yangyxt over 2 years ago - 1 comment
Labels: enhancement, help wanted

#487 - can sambamba markdup give duprate concrete number?

Issue - State: open - Opened by asmlgkj over 2 years ago
Labels: bug

#486 - sambamba --version's output doubled

Issue - State: open - Opened by kim-fehl over 2 years ago - 1 comment
Labels: bug

#485 - `Samtools + libdeflate` out performs `sambamba` on a single thread

Issue - State: open - Opened by mebbert over 2 years ago - 3 comments
Labels: enhancement

#484 - Sambamba has remaining references to libbiod

Issue - State: closed - Opened by tillea almost 3 years ago - 9 comments
Labels: bug

#483 - markdup - segmentation fault

Issue - State: closed - Opened by BioinfoRDX almost 3 years ago - 1 comment
Labels: bug

#482 - Cannot build 0.8.1 with Guix

Issue - State: closed - Opened by rekado almost 3 years ago - 7 comments
Labels: bug

#481 - do you support aggregation and dedup in one command?

Issue - State: closed - Opened by AlisaGU about 3 years ago - 3 comments
Labels: support request - please use google groups instead

#480 - Made compile with removed alias this in Nullable

Pull Request - State: closed - Opened by dukc about 3 years ago - 3 comments

#479 - Support filtering of absolute template length

Pull Request - State: closed - Opened by tolot27 over 3 years ago - 2 comments

#478 - Fix build when GCC is not installed

Pull Request - State: closed - Opened by stephank over 3 years ago - 1 comment

#476 - sambamba-markdup: Unexpected '-' when converting from type string to type ulong

Issue - State: open - Opened by ls233 over 3 years ago - 1 comment
Labels: support request - please use google groups instead

#475 - sambamba markdup: Unable to write to stream

Issue - State: closed - Opened by sklages over 3 years ago - 1 comment
Labels: bug

#474 - Inaccessible google groups support forum

Issue - State: closed - Opened by Poshi over 3 years ago - 2 comments
Labels: Follow the checklist to report an issue

#473 - Compiling from source v.0.8.0 fails

Issue - State: closed - Opened by nadyawilliams over 3 years ago - 2 comments
Labels: support request - please use google groups instead

#472 - MultiQC support for sambamba markdup

Issue - State: closed - Opened by gartician over 3 years ago - 3 comments
Labels: enhancement, markdup, specification

#471 - downsampling by sambamba with seed

Issue - State: open - Opened by dulunar over 3 years ago - 1 comment
Labels: support request - please use google groups instead

#470 - sambamba merge using too much memory

Issue - State: closed - Opened by Poshi over 3 years ago - 1 comment
Labels: support request - please use google groups instead

#469 - disable linking of default shared libs on static build

Pull Request - State: closed - Opened by tolot27 over 3 years ago - 1 comment

#468 - add missing standard SAM header tags

Pull Request - State: closed - Opened by tolot27 over 3 years ago - 1 comment

#467 - depth error

Issue - State: open - Opened by Masaru-iehisa over 3 years ago
Labels: support request - please use google groups instead, Follow the checklist to report an issue

#466 - Is it necessary to sort bam files by read names before markdup?

Issue - State: open - Opened by xiekunwhy over 3 years ago
Labels: support request - please use google groups instead

#465 - could not make sambamba-ldmd2-64

Issue - State: closed - Opened by An1e over 3 years ago - 1 comment
Labels: support request - please use google groups instead

#464 - Sambamba should be able to convert SAM->BAM and sort at the same time like samtools

Issue - State: closed - Opened by moldach almost 4 years ago - 1 comment
Labels: bug

#463 - sambamba markdup deadlock in Ubuntu 14.04

Issue - State: open - Opened by dulunar almost 4 years ago - 3 comments
Labels: bug, markdup, hard to reproduce, help wanted

#462 - additional header columns are removed

Issue - State: closed - Opened by tolot27 almost 4 years ago - 1 comment
Labels: bug, newbie, easy, specification, help wanted, reproducible!

#461 - markduplicate's result still differs from picard

Issue - State: closed - Opened by xiucz almost 4 years ago - 1 comment

#460 - Fix meson build

Issue - State: closed - Opened by pjotrp almost 4 years ago - 1 comment
Labels: bug

#459 - Make install error

Issue - State: closed - Opened by Stikus almost 4 years ago - 2 comments
Labels: in progress, Installation

#458 - Sambamba depth -q error

Issue - State: open - Opened by MatthieuBeukers almost 4 years ago - 2 comments
Labels: bug, reproducible!

#457 - Sambamba depth tools does not report softclipped bases

Issue - State: closed - Opened by robinpaul85 about 4 years ago
Labels: support request - please use google groups instead

#456 - sambamba depth -m

Issue - State: closed - Opened by aledj2 about 4 years ago - 1 comment

#455 - Differences in output between depth region -m (v0.6.5 and v0.7.1)

Issue - State: closed - Opened by RachelDuffin about 4 years ago - 1 comment

#454 - Update INSTALL.md

Pull Request - State: closed - Opened by samsonjm over 4 years ago - 1 comment

#453 - sambamba sort error with sambamba-0.7.1-linux-static

Issue - State: closed - Opened by WellJoea over 4 years ago - 2 comments

#452 - option not to print warning messages (eg re overlapping mates)

Issue - State: closed - Opened by aledj2 over 4 years ago - 3 comments

#451 - Limiting ram usage in merge?

Issue - State: closed - Opened by ghost over 4 years ago - 1 comment

#450 - Feature request: Build sambamba with libdeflate

Issue - State: closed - Opened by rhpvorderman over 4 years ago - 3 comments
Labels: enhancement

#449 - Sambamba not running in OSX Catalina

Issue - State: closed - Opened by juulluu21 over 4 years ago - 2 comments
Labels: support request - please use google groups instead

#448 - gold linker with guix ignores rpath

Issue - State: closed - Opened by pjotrp over 4 years ago - 1 comment

#446 - exclude softclipped bases from the reported depth

Issue - State: closed - Opened by aledj2 over 4 years ago - 2 comments

#445 - sambamba depth output coordinate system

Issue - State: closed - Opened by tahuh over 4 years ago - 2 comments

#444 - Filtering out reads with not and 2 conditions

Issue - State: closed - Opened by paulstretenowich over 4 years ago - 1 comment

#441 - compilation error: no identifier for declarator Usage

Issue - State: closed - Opened by adily777 over 4 years ago - 3 comments

#439 - Memory issue with Sambamba markdup

Issue - State: closed - Opened by psur9757 over 4 years ago
Labels: Follow the checklist to report an issue

#438 - Installation issue with BioD

Issue - State: closed - Opened by hildebs42 over 4 years ago
Labels: support request - please use google groups instead

#433 - sambamba-depth: couldn't open file

Issue - State: closed - Opened by linelieblein over 4 years ago - 2 comments

#432 - Discrepancy between samtools depth and Sambamba region

Issue - State: closed - Opened by wynstep over 4 years ago - 2 comments
Labels: Follow the checklist to report an issue

#428 - bug when downsampling twice with the same seed

Issue - State: closed - Opened by isthisthat over 4 years ago - 3 comments

#427 - markdup: Barcode-aware duplicate marking

Issue - State: closed - Opened by pontushojer almost 5 years ago - 2 comments
Labels: enhancement, help wanted

#426 - sambamba depth window -L region support

Issue - State: closed - Opened by isthisthat almost 5 years ago - 1 comment
Labels: enhancement

#425 - Sambamba with htslib 1.10.2

Issue - State: closed - Opened by bioinfornatics almost 5 years ago - 4 comments

#424 - Incompatible with OSX Catalina

Issue - State: closed - Opened by danielecook almost 5 years ago - 5 comments

#423 - Discrepancy between sambamba and samtools

Issue - State: closed - Opened by sybrohee almost 5 years ago - 2 comments

#422 - Please port tools and test suite to Python3

Issue - State: closed - Opened by tillea almost 5 years ago - 2 comments
Labels: bug

#421 - sambamba-markdup: not enough data in stream via /dev/stdin

Issue - State: open - Opened by heuermh almost 5 years ago - 15 comments
Labels: enhancement, markdup, reproducible!

#417 - bed file input for sambamba dept filter outputing unrequested position?

Issue - State: closed - Opened by duartemolha almost 5 years ago - 2 comments

#416 - Error: undefined identifier

Issue - State: closed - Opened by kalon33 almost 5 years ago - 3 comments

#415 - Feature request: absolute value operator in filter statements

Issue - State: closed - Opened by tzuni almost 5 years ago - 1 comment

#410 - filtering uniquely mapped reads results in odd number of reads in PE data

Issue - State: closed - Opened by rikrdo89 about 5 years ago - 1 comment
Labels: enhancement

#406 - sambamba depth region -L <(expression) bam segfaults

Issue - State: open - Opened by isthisthat over 5 years ago - 10 comments
Labels: bug, reproducible!

#404 - Add option to output in csv format

Pull Request - State: closed - Opened by SichongP over 5 years ago - 4 comments

#399 - Compile Sambamba with DIP1000

Issue - State: closed - Opened by pjotrp over 5 years ago - 2 comments

#395 - sambamba depth window sementation fault [core dump] using --combined flag

Issue - State: closed - Opened by iamh2o over 5 years ago - 1 comment
Labels: waiting for response

#393 - markdup segmentation fault

Issue - State: closed - Opened by ZhifeiLuo over 5 years ago - 66 comments
Labels: bug, in progress, important

#391 - Slice test case fails

Issue - State: closed - Opened by pjotrp over 5 years ago - 1 comment

#382 - Use different test frame work

Issue - State: closed - Opened by pjotrp almost 6 years ago - 1 comment
Labels: enhancement

#372 - Update sambamba documentation

Issue - State: closed - Opened by pjotrp about 6 years ago - 1 comment
Labels: Documentation