Andreas Tille pushed to branch master at Debian Med / dnarrange
Commits: ab8af239 by Andreas Tille at 2022-07-19T11:53:29+02:00 routine-update: New upstream version - - - - - 978a034b by Andreas Tille at 2022-07-19T11:58:56+02:00 New upstream version 1.5.3 - - - - - c5e74ca4 by Andreas Tille at 2022-07-19T11:59:04+02:00 Update upstream source from tag 'upstream/1.5.3' Update to upstream version '1.5.3' with Debian dir 36e39ef6ddd7aba5fc010ed94fffc3652f1b01c3 - - - - - 162a4c72 by Andreas Tille at 2022-07-19T11:59:23+02:00 routine-update: Remove trailing whitespace in debian/control - - - - - f740dde4 by Andreas Tille at 2022-07-19T11:59:26+02:00 Apply multi-arch hints. + dnarrange: Add Multi-Arch: foreign. Changes-By: apply-multiarch-hints - - - - - ceb7609e by Andreas Tille at 2022-07-19T11:59:56+02:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - README.md - debian/changelog - debian/control - setup.py Changes: ===================================== README.md ===================================== @@ -109,12 +109,12 @@ and [MAFFT][] to be installed). Then re-[align](https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md) -the merged reads to the genome (it's recommended to do this without -repeat-masking): +the merged reads to the genome (maybe using e.g. `-m20` or `-m50` to +make it more sensitive-but-slow): lastdb -P8 -uNEAR mydb genome.fa last-train -P8 mydb merged.fa > merged.par - lastal -P8 -p merged.par mydb merged.fa | last-split > merged.maf + lastal -P8 -m20 --split -p merged.par mydb merged.fa > merged.maf And draw pictures: @@ -266,7 +266,7 @@ You can get the rearranged reads, without merging them, like this: dnarrange-merge all-reads.fq groups.maf > some-reads.fq This may be useful if you wish to re-align the rearranged reads to the -genome more slowly-and-carefully (e.g. without repeat-masking). +genome more slowly-and-carefully. `dnarrange-merge` also has options that it passes to `lamassemble`: you can see them with `dnarrange-merge --help`, and they're described ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +dnarrange (1.5.3-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Remove trailing whitespace in debian/control (routine-update) + + -- Andreas Tille <[email protected]> Tue, 19 Jul 2022 11:59:27 +0200 + dnarrange (1.5.2-1) unstable; urgency=medium * Add upstream/metadata ===================================== debian/control ===================================== @@ -4,7 +4,7 @@ Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Nilesh Patra <[email protected]>, -Build-Depends: +Build-Depends: debhelper-compat (= 13), dh-python, python3-all, @@ -21,6 +21,7 @@ Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}, +Multi-Arch: foreign Description: Method to find rearrangements in long DNA reads relative to a genome seq This package provides utilities to align the reads to the genome, find rearrangements and draw pictures of rearranged groups ===================================== setup.py ===================================== @@ -1,6 +1,6 @@ import setuptools -commitInfo = " (HEAD -> master, tag: 1.5.2)".strip("( )").split() +commitInfo = " (HEAD -> master, tag: 1.5.3)".strip("( )").split() version = commitInfo[commitInfo.index("tag:") + 1].rstrip(",") setuptools.setup( View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/compare/156fc81ab7f37977ae3c8ef9f2b79adf2d8d89de...ceb7609ea155a32fcede1a54f0060e96488b28e3 -- View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/compare/156fc81ab7f37977ae3c8ef9f2b79adf2d8d89de...ceb7609ea155a32fcede1a54f0060e96488b28e3 You're receiving this email because of your account on salsa.debian.org.
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