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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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sorting of loci file for dense-snps #58

Open nurmians opened 5 years ago

nurmians commented 5 years ago

sort -k1,1 -n 2,2n loci_unsrt.tsv > losi_sorted.tsv does not work. Did you mean: sort -k1,1n -k 2,2n loci_unsrt.tsv > losi_sorted.tsv or sort -k1,1 -k2,2n loci_unsrt.tsv > losi_sorted.tsv

Either way, it would be better just to say if you want the chromosomes in alphabetical or numerical (natural) order.

nurmians commented 5 years ago

Looks like the output of alleleCounter is identical for both inputs (alphabetical and numerically sorted).