samclip 0.4.0-3 source package in Ubuntu
Changelog
samclip (0.4.0-3) unstable; urgency=medium
* Team upload.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* Apply multi-arch hints.
+ samclip: Add Multi-Arch: foreign.
-- Étienne Mollier <email address hidden> Wed, 13 Oct 2021 22:25:59 +0200
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 | Published | Component | Section | |
|---|---|---|---|---|
| Kinetic | release | universe | misc | |
| Jammy | release | universe | misc |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| samclip_0.4.0-3.dsc | 1.9 KiB | abbf164b522f46b3dcb0f2bed3ba37e836f8c66b63b192ca08392be27c4d60bc |
| samclip_0.4.0.orig.tar.gz | 35.5 KiB | 8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127 |
| samclip_0.4.0-3.debian.tar.xz | 3.7 KiB | 6b1669d2e617aafba794ecc2d81527cb3528a9d3c4548697614834be071eaf95 |
Available diffs
- diff from 0.4.0-2 to 0.4.0-3 (858 bytes)
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.
