[med-svn] [Git][med-team/dnarrange][master] 6 commits: routine-update: New upstream version

[Andreas Tille (@tille)]

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 <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
 Uploaders:
  Nilesh Patra <nilesh at debian.org>,
-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
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