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more command line help

This commit is contained in:
Heng Li 2014-11-04 15:41:18 -05:00
parent e5d7f4fc30
commit 2a41772d0a
1 changed files with 5 additions and 2 deletions
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7
bwa-typeHLA.js
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@ -56,10 +56,13 @@ while ((c = getopt(arguments, "l:d:")) != null) {
} }
if (arguments.length == getopt.ind) { if (arguments.length == getopt.ind) {
print(""); print("");
print("Usage: k8 bwa-typeHLA.js [options] <HLA-to-contig.sam>\n"); print("Usage: k8 bwa-typeHLA.js [options] <exon-to-contig.sam>\n");
print("Options: -d INT drop a contig if the edit distance to the closest gene is >INT ["+thres_nm+"]"); print("Options: -d INT drop a contig if the edit distance to the closest gene is >INT ["+thres_nm+"]");
print(" -l INT drop a contig if its match too short ["+thres_len+"]"); print(" -l INT drop a contig if its match too short ["+thres_len+"]");
print(""); print("");
print("Note: The output is TAB delimited with each line consisting of allele1, allele2,");
print(" #mismatches/gaps on primary exons, #mismatches/gaps on other exons and");
print(" #exons used in typing.");
exit(1); exit(1);
} }
@ -265,4 +268,4 @@ for (var i = 0; i < glist.length; ++i)
out.sort(function(a, b) { return a[0]!=b[0]? a[0]-b[0] : a[1]!=b[1]? b[1]-a[1] : a[4]!=b[4]? a[4]-b[4] : a[2]!=b[2]? a[2]-b[2] : a[3]-b[3]}); out.sort(function(a, b) { return a[0]!=b[0]? a[0]-b[0] : a[1]!=b[1]? b[1]-a[1] : a[4]!=b[4]? a[4]-b[4] : a[2]!=b[2]? a[2]-b[2] : a[3]-b[3]});
for (var i = 0; i < out.length; ++i) for (var i = 0; i < out.length; ++i)
print(glist[out[i][2]], glist[out[i][3]], out[i][0]>>8&0xff, out[i][0]&0xff, out[i][1]); print(glist[out[i][3]], glist[out[i][2]], out[i][0]>>8&0xff, out[i][0]&0xff, out[i][1]);