readCounter function from HMMcopy utilities, used to generate read in windows
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
bai{:bash}
BAM/CRAM index file
*.{bai}
meta2{:bash}
fasta{:bash}
Genome fasta file. Required when using a CRAM file.
wig{:bash}
*.wig{:bash}
A wig file with the number of reads lying within each window in each chromosome
*.wig
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
