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