jvarkit

HmmMergeBed

For @154sns. Merge hmm bed

Usage

Usage: hmmmergebed [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -n, --num
      dictionary if data are sorted on a REF order.
      Default: -1
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference, --dict
      optional dictionary if data are sorted on a REF order.A SAM Sequence 
      dictionary source: it can be a *.dict file, a fasta file indexed with 
      'picard CreateSequenceDictionary', or any hts file containing a 
      dictionary (VCF, BAM, CRAM, intervals...)
    --version
      print version and exit
    -u
      Hide invalid lines
      Default: false

Keywords

• bed
• merge

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew hmmmergebed

The java jar file will be installed in the dist directory.

Creation Date

20191108

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/hmm/HmmMergeBed.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/hmm/HmmMergeBedTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite hmmmergebed ? 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

input

input is a set of sorted BED file , or a file with the ‘.list’ suffix containing the paths to the bed file.

Example:

$ head -n 3  ~/DC10* 
==> DC1074_UCSC.bed.txt <==
chr22	0	64000	6_Heterochrom_lowsignal
chr22	64000	65400	1_Polycomb_repressed
chr22	65400	119600	6_Heterochrom_lowsignal

==> DC1076_UCSC.bed.txt <==
chr22	0	119600	6_Heterochrom_lowsignal
chr22	119600	120000	3_Weak_promoter
chr22	120000	120200	4_Active_promoter

==> DC1077_UCSC.bed.txt <==
chr22	0	118400	7_Heterochrom_lowsignal
chr22	118400	119600	1_Polycomb_repressed
chr22	119600	120200	2_Poised_promoter

==> DC1082_UCSC.bed.txt <==
chr22	0	119600	6_Heterochrom_lowsignal
chr22	119600	120200	3_Weak_promoter
chr22	120200	122200	6_Heterochrom_lowsignal


$ java -jar dist/hmmmergebed.jar -n 3 ~/DC10*.txt 
chr22	0	64000	6_Heterochrom_lowsignal
#chr22	64000	65400	1_Polycomb_repressed:1;6_Heterochrom_lowsignal:2;7_Heterochrom_lowsignal:1
chr22	65400	119600	6_Heterochrom_lowsignal
chr22	119600	120000	3_Weak_promoter
#chr22	120000	120200	2_Poised_promoter:1;3_Weak_promoter:1;4_Active_promoter:2
#chr22	120200	120400	1_Polycomb_repressed:1;3_Weak_promoter:1;4_Active_promoter:1;6_Heterochrom_lowsignal:1
chr22	120400	122000	6_Heterochrom_lowsignal
chr22	122000	122600	3_Weak_promoter
#chr22	122600	122800	3_Weak_promoter:2;6_Heterochrom_lowsignal:2
chr22	122800	130000	6_Heterochrom_lowsignal
(...)

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