[med-svn] [Git][med-team/mapdamage][master] 9 commits: New upstream version 2.2.1+dfsg
Steffen Möller
gitlab at salsa.debian.org
Mon Jun 29 23:27:28 BST 2020
Steffen Möller pushed to branch master at Debian Med / mapdamage
Commits:
a9e55a3f by Steffen Moeller at 2020-06-30T00:19:26+02:00
New upstream version 2.2.1+dfsg
- - - - -
2b0f7dbf by Steffen Moeller at 2020-06-30T00:19:26+02:00
routine-update: New upstream version
- - - - -
a9183ef7 by Steffen Moeller at 2020-06-30T00:19:26+02:00
Update upstream source from tag 'upstream/2.2.1+dfsg'
Update to upstream version '2.2.1+dfsg'
with Debian dir ec833f08eed026cce3b5bf83a617566c9bb0b0da
- - - - -
a977ce61 by Steffen Moeller at 2020-06-30T00:19:27+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
3a2b9ba2 by Steffen Moeller at 2020-06-30T00:19:27+02:00
routine-update: debhelper-compat 13
- - - - -
1d67166f by Steffen Moeller at 2020-06-30T00:19:33+02:00
routine-update: Add salsa-ci file
- - - - -
bde56cdd by Steffen Moeller at 2020-06-30T00:19:33+02:00
routine-update: Rules-Requires-Root: no
- - - - -
8df98553 by Steffen Moeller at 2020-06-30T00:19:36+02:00
Set upstream metadata fields: Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
1faef07a by Steffen Moeller at 2020-06-30T00:26:20+02:00
New upstream version.
- - - - -
9 changed files:
- README.md
- bin/mapDamage
- debian/changelog
- debian/control
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- mapdamage/version.py
- setup.py
Changes:
=====================================
README.md
=====================================
@@ -1,29 +1,33 @@
## mapDamage
-[](http://bioconda.github.io/recipes/mapdamage2/README.html) [](https://anaconda.org/bioconda/mapdamage2/files)   [](https://www.repostatus.org/#inactive)
+[](http://bioconda.github.io/recipes/mapdamage2/README.html) [](https://anaconda.org/bioconda/mapdamage2/files)
+  [](https://www.repostatus.org/#inactive)
#### `bioconda` installation
-- python3 version **2.2.0**
-```
-conda install -c bioconda mapdamage2=2.2.0
-```
+* python3 version **2.2.1**
-- python3 version **2.2.0** **with** R and 4 mandatory packages for the Bayesian inference:
+```
+conda install -c bioconda mapdamage2=2.2.1
```
-conda install -c bioconda mapdamage2=2.2.0=pyr36_1
+
+* python3 version **2.2.1** **with** R and 4 mandatory packages for the Bayesian inference:
+
+```
+conda install -c bioconda mapdamage2=2.2.1=pyr36_1
```
---
### Important
-- From version `2.2.0` the `master` branch is requiring **python3** as `python2` is not supported from 2020-01-01.
+* From version `2.2.1` the `master` branch is requiring **python3** as `python2` is not supported from 2020-01-01.
-- Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of `mapDamage` to use half of the data for estimation of the damage parameters, sorry for the inconvenience..
+* Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of `mapDamage` to use half of the data for estimation of the damage parameters, sorry for the inconvenience..
### Introduction
+
Complete documentation, instructions, examples, screenshots and FAQ are available at [this address](http://ginolhac.github.io/mapDamage/).
[mapDamage2](https://geogenetics.ku.dk/publications/mapdamage2.0/) is a computational framework written in **Python3** and **R**, which tracks and quantifies DNA damage patterns
@@ -31,31 +35,30 @@ among ancient DNA sequencing reads generated by Next-Generation Sequencing platf
`mapDamage` was developed at the [Centre for GeoGenetics](https://geogenetics.ku.dk/) by the [Orlando Group ](https://geogenetics.ku.dk/research_groups/palaeomix_group/).
-
### Citation
+
If you use this program, please cite the following publication:
Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
[mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
_Bioinformatics_ 23rd April 2013. doi: 10.1093/bioinformatics/btt193](http://bioinformatics.oxfordjournals.org/content/early/2013/05/17/bioinformatics.btt193)
-
The original `mapDamage1` was published in the following article:
Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L.
[mapDamage: testing for damage patterns in ancient DNA sequences. _Bioinformatics_ 2011 **27**(15):2153-5
http://bioinformatics.oxfordjournals.org/content/27/15/2153](http://bioinformatics.oxfordjournals.org/content/27/15/2153)
-
### Test the no-stats part and rescaling
you can test `mapDamage` by running:
-```
+```
cd mapDamage/mapdamage/
python3 mp_test.py
```
should return
-```
+
+```
Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats
Reading from 'tests/test.bam'
Writing results to 'tests/results/'
@@ -69,7 +72,7 @@ Ran 2 tests in 3.357s
OK
```
-
### Contact
+
Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email:
ginolhac at gmail.com, mikkelsch at gmail.com or jonsson.hakon at gmail.com.
=====================================
bin/mapDamage
=====================================
@@ -139,20 +139,6 @@ def _check_mm_option():
raise SystemExit("The --mapdamage-modules path (path=%s) must contain the mapdamage module" % path_to_mm)
return path_to_mm
-def is_paired(alignfile):
- """
- check if an alignment file contains paired end data by
- looking at the first 100 reads
- """
-
- n = 0
- for read in alignfile:
- if read.is_paired:
- return True
- n += 1
- if n == 100:
- return False
-
def main():
start_time = time.time()
@@ -241,14 +227,6 @@ def main():
else:
in_bam = pysam.Samfile(options.filename)
- # exit SAM/BAM is paired (look at top 100 reads)
- if is_paired(in_bam):
- logger.error("alignment file must be single-ended")
- sys.stderr.write("alignment file must be single-ended\n")
- sys.exit(1)
- # reset SAM/BAM to the begining
- in_bam = pysam.Samfile(options.filename)
-
reflengths = dict(list(zip(in_bam.references, in_bam.lengths)))
# check if references in SAM/BAM are the same in the fasta reference file
fai_lengths = mapdamage.seq.read_fasta_index(options.ref + ".fai")
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+mapdamage (2.2.1+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Submit, Repository,
+ Repository-Browse (routine-update)
+ * d/rules: Improved post-build cleansing
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 30 Jun 2020 00:19:37 +0200
+
mapdamage (2.2.0+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
python3,
dh-python,
python3-setuptools,
@@ -13,10 +13,11 @@ Build-Depends: debhelper-compat (= 12),
r-cran-gam <!nocheck>,
r-cran-ggplot2 <!nocheck>,
r-cran-inline <!nocheck>
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/mapdamage
Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git
Homepage: https://ginolhac.github.io/mapDamage/
+Rules-Requires-Root: no
Package: mapdamage
Architecture: all
=====================================
debian/rules
=====================================
@@ -27,3 +27,5 @@ override_dh_python3:
override_dh_auto_clean:
dh_auto_clean
rm -f mapdamage/_version.py
+ rm -f mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Length_plot.pdf mapdamage/tests/results/Length_plot.pdf
+ rm -f mapdamage/tests/fake1.fasta.fai mapdamage/tests/results/3pGtoA_freq.txt mapdamage/tests/results/5pCtoT_freq.txt mapdamage/tests/results/Runtime_log.txt mapdamage/tests/results/dnacomp.txt mapdamage/tests/results/lgdistribution.txt mapdamage/tests/results/misincorporation.txt mapdamage/tests/test.rescaled.sam
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Submit: https://github.com/ginolhac/mapDamage/issues/new
Reference:
- Author: >
Hákon Jónsson and Aurélien Ginolhac and Mikkel Schubert and
@@ -26,3 +27,5 @@ Registry:
- Name: conda:bioconda
Entry: mapdamage2
Bug-Database: https://github.com/ginolhac/mapDamage/issues
+Repository: https://github.com/ginolhac/mapDamage.git
+Repository-Browse: https://github.com/ginolhac/mapDamage
=====================================
mapdamage/version.py
=====================================
@@ -2,4 +2,4 @@
try:
from mapdamage._version import __version__
except ImportError:
- __version__ = "2.2.0"
+ __version__ = "2.2.1"
=====================================
setup.py
=====================================
@@ -35,7 +35,7 @@ def setup_version():
version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))
with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
handle.write("#!/usr/bin/env python\n")
- handle.write("__version__ = %r\n" % (version.strip(),))
+ handle.write("__version__ = %r\n" % (version.decode("utf-8").strip(),))
except (subprocess.CalledProcessError, OSError) as error:
raise SystemExit("Could not determine mapDamage version: %s" % (error,))
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/90380206100e9dd6c74af3b0deae952371ccbcbd...1faef07a2d8b4839f0d5ec7e2a44b81caef5620c
--
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/90380206100e9dd6c74af3b0deae952371ccbcbd...1faef07a2d8b4839f0d5ec7e2a44b81caef5620c
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