[med-svn] [Git][med-team/dnarrange][upstream] New upstream version 1.5.3

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / dnarrange


Commits:
978a034b by Andreas Tille at 2022-07-19T11:58:56+02:00
New upstream version 1.5.3
- - - - -


2 changed files:

- README.md
- 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


=====================================
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/-/commit/978a034b2890501a402d6e222b5dc5ba9b645727

-- 
View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/commit/978a034b2890501a402d6e222b5dc5ba9b645727
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220719/bbf13c57/attachment-0001.htm>