Support bedGraph output in only-depth

[ghuls]

Support bedGraph output in only-depth:

This is basically perbase -z output without header and chromosomes sorted by lexographically.

This would allow to create bigwig files relatively easily. (naive sorting takes quite a while instead of reading the reads by chromosome in lexographical order).

perbase only-depth -z ${bam} | tail -n +2 | LC_COLLATE=C sort -k 1,1 -k 2,2n -k 3,3n > ${bedgraph}

bedGraphToBigWig ${bedgraph} ${chrom_sizes} ${bigwig}

bedGraph format: http://genome.ucsc.edu/goldenPath/help/bedgraph.html

[sstadick]

I'll looking into making this more natively supported. There is also the --bed-format option which, with -z should make the output more BED like. The output order is currently dictated by the BAM header, if the input BAM is sorted lexographically then so will the output of perbase (not ideal, I'm just noting it).

Options to make this work would be:

• Add a "lexographical sort" flag that sorts the BAM header before processing, this could be fine...but I could see it still resulting in slightly different sort orders than what is needed downstream.
• Add support for outputing in the same order as an input BED file or sequence dictionary. This probably provides the most flexibility / explicitness
• Add an optional input that is just a list of chromosome names that represent the order things should be output. meh