Sliding Window : discriminate partial and fully contained fragments (from a bam file)
Usage: biostar234230 [options] Files
Options:
-filter, --filter
A filter expression. Reads matching the expression will be filtered-out.
Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj
for a complete syntax.
Default: mapqlt(1) || MapQUnavailable() || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment()
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
-s, --winshift
Shift each window by 's' bases
Default: 50
-w, --winsize
Window size
Default: 100
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar234230
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite biostar234230 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example:
$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110915_CEUtrio_b37_decoy_alignment/CEUTrio.HiSeq.WGS.b37_decoy.NA12892.clean.dedup.recal.bam" | java -jar dist/biostar234230.jar
#contig start end pairs_in_window pairs_over_window pairs_partial_overlap
1 10000 10100 0 2 240
1 10050 10150 4 615 274
1 10100 10200 0 800 276
1 10150 10250 0 216 649
1 10200 10300 0 2982 809
1 10250 10350 0 2918 207
1 10300 10400 0 1923 2851
1 10350 10450 0 227 4498
1 10400 10500 0 31 1971
(...)