Ubuntu
samclip package

samclip 0.4.0-4 source package in Ubuntu

Changelog

samclip (0.4.0-4) unstable; urgency=medium

  * d/watch: adjust to github change; move to git mode.
  * d/control: add myself to uploaders.
  * d/control: declare compliance to standards version 4.6.1.

 -- Étienne Mollier <email address hidden>  Sun, 06 Nov 2022 19:34:38 +0100

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
all
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Oracular release universe misc
Noble release universe misc
Mantic release universe misc
Lunar release universe misc

Builds

Lunar: [FULLYBUILT] amd64

Downloads

File Size SHA-256 Checksum
samclip_0.4.0-4.dsc 2.1 KiB b5b2ace535a0964a020a0bd6da347ebfd3908e795159d15b93bc9d7c54a54125
samclip_0.4.0.orig.tar.gz 35.5 KiB 8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127
samclip_0.4.0-4.debian.tar.xz 3.8 KiB 1c2d81f4eae35d58d1c230d251298d1924fc6c69243368497d60722fa3872755

Available diffs

No changes file available.

Binary packages built by this source

samclip: filter SAM file for soft and hard clipped alignments

 Most short read aligners perform local alignment of reads to the
 reference genome. Examples includes bwa mem, minimap2, and bowtie2
 (unless in --end-to-end mode). This means the ends of the read may not
 be part of the best alignment.
 .
 This can be caused by:
 .
  * adapter sequences (aren't in the reference)
  * poor quality bases (mismatches only make the alignment score worse)
  * structural variation in your sample compared to the reference
  * reads overlapping the start and end of contigs (including
    circular genomes)
 .
 Read aligners output a SAM file. Column 6 in this format stores the
 CIGAR string. which describes which parts of the read aligned and which
 didn't. The unaligned ends of the read can be "soft" or "hard" clipped,
 denoted with S and H at each end of the CIGAR string. It is possible for
 both types to be present, but that is not common. Soft and hard don't
 mean anything biologically, they just refer to whether the full read
 sequence is in the SAM file or not.