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
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 -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
(?i)bam will capture
foo.BAM. This is standard regular expression
syntax unrelated to ASCIIGenome.
Note that the command
seqRegex by default is case insensitive, unless
-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?¶
&& 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?¶
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