Package: artfastqgenerator / 0.0.20150519-3

adapt_doc.patch Patch series | download
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Author: Andreas Tille <tille@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