[med-svn] [artfastqgenerator] 06/09: Adapt usage hint to how it is used on Debian

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository artfastqgenerator.

commit cdee7cf08f16b4de1de9247e0039152b817f7004
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jan 14 14:08:31 2017 +0100

    Adapt usage hint to how it is used on Debian
---
 debian/changelog               |  1 +
 debian/patches/adapt_doc.patch | 24 ++++++++++++++++++++++++
 debian/patches/series          |  1 +
 3 files changed, 26 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index b2263e4..96e0d41 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,7 @@ artfastqgenerator (0.0.20150519-2) UNRELEASED; urgency=medium
   * cme fix dpkg-control
   * for some strange reason autopkgtest fails when using a symlink to the
     jar - so rather use a wrapper
+  * Adapt usage hint to how it is used on Debian
 
  -- Andreas Tille <tille at debian.org>  Sat, 14 Jan 2017 11:50:59 +0100
 
diff --git a/debian/patches/adapt_doc.patch b/debian/patches/adapt_doc.patch
new file mode 100644
index 0000000..4719ed6
--- /dev/null
+++ b/debian/patches/adapt_doc.patch
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 14 Jan 2017 11:50:59 +0100
+Description: Adapt usage hint to how it is used on Debian
+
+--- a/README.txt
++++ b/README.txt
+@@ -44,7 +44,7 @@ Unzipping ArtificialFastqGenerator.zip w
+ ArtificialFastqGenerator can be run with any reference sequence in FASTA format. Below is information about all of its user
+ parameters:
+ 
+-usage java -jar ArtificialFastqGenerator.jar -O <outputPath> -R <referenceGenomePath> -S <startSequenceIdentifier>
++usage: artificialfastqgenerator -O <outputPath> -R <referenceGenomePath> -S <startSequenceIdentifier>
+ -F1 <fastq1ForQualityScores> -F2 <fast2ForQualityScores> -CMGCS <coverageMeanGCcontentSpread> -CMP <coverageMeanPeak>
+ -CMPGC <coverageMeanPeakGCcontent> -CSD <coverageSD> -E <endSequenceIdentifier> -GCC <GCcontentBasedCoverage>
+ -GCR <GCcontentRegionSize> -L <logRegionStats> -N <nucleobaseBufferSize> -OF <outputFormat> -RCNF <readsContainingNfilter>
+@@ -84,7 +84,7 @@ accepting Phred quality scores from test
+ should include the file base name (e.g. $OUTPUT_DIR/Chr1), and the -S and -E parameters are prefixes of the desired sequence
+ identifiers, sufficiently long to ensure a match.
+ 
+-java -jar ArtificialFastqGenerator.jar -R miniReference.fasta -O C1 -S ">1" -E ">" -URQS true -SE true -F1 test1.fastq -F2 test2.fastq
++   artificialfastqgenerator -R miniReference.fasta -O C1 -S ">1" -E ">" -URQS true -SE true -F1 test1.fastq -F2 test2.fastq
+ 
+ Apart from the artificial FASTQs, ArtificialFastqGenerator will output a file which contains the start and end indexes in the
+ reference sequence of all the generated reads, and a log file which contains the parameter settings and summary coverage and
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..91670fe
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+adapt_doc.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/artfastqgenerator.git