FAQ and miscellanea

Can I change colour theme / Can I use my configuration?

To change colour theme use the -c/--config command line option or the interactive command setConfig. To make your own theme and set it as default, use as template one of the files in the repository directory config, edit it as desired and save it as ~/.asciigenome_config.


ASCIIGenome -c metal ...    <- Use the "metal" built-in them
ASCIIGenome -c mytheme.conf <- Read configuration from this file
ASCIIGenome ...             <- No args to -c: Read file ~/.asciigenome_config or use default theme

For available colour names see the help in colorTrack or this cheat sheet.

Can I turn off case sensitivity?

For command that do not explicitly enable turning on or off case sensitivity, you can prepend (?i) to your regex to match in case insensitve mode, e.g. (?i)bam will capture foo.bam and foo.BAM. This is standard regular expression syntax unrelated to ASCIIGenome.

Note that the command seqRegex by default is case insensitive, unless the flag -c is set.

Why reads and coverage in bam tracks sometimes disappear?

When displaying bam files, ASCIIGenome is configured to disable the coverage and read tracks if the window size is >100,000 bp. This is to prevent the browsing to become too slow. To display such large windows consider bigWig or tdf file format.

Can I execute multiple commands inside -x/--exec or at the command prompt?

Use the && to concatenate commands (similar to Unix syntax). E.g. colorTrack red && goto chr1:150000 && zo.

How can I print the header of a VCF file?

Assuming bcftools is available, use the sys command, for example:

sys bcftools view -H my_variants.vcf.gz | less

Of course you can further parse the header by piping to standard Unix tools. For example, to exclude the contig lines use:

sys bcftools view -h mutect/WW00282.vcf.gz | grep -v '##contig' | less