From 2a41772d0a94e08e2467281cea4cc2242c5c0dc0 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 4 Nov 2014 15:41:18 -0500 Subject: [PATCH] more command line help --- bwa-typeHLA.js | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/bwa-typeHLA.js b/bwa-typeHLA.js index fa35199..cdcbbd3 100644 --- a/bwa-typeHLA.js +++ b/bwa-typeHLA.js @@ -56,10 +56,13 @@ while ((c = getopt(arguments, "l:d:")) != null) { } if (arguments.length == getopt.ind) { print(""); - print("Usage: k8 bwa-typeHLA.js [options] \n"); + print("Usage: k8 bwa-typeHLA.js [options] \n"); 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(""); + 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); } @@ -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]}); 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]);