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CLI help

This commit is contained in:
Heng Li 2014-10-21 00:22:59 -04:00
parent 497913d404
commit 2bfa3c767b
1 changed files with 8 additions and 7 deletions
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15
bwa-postalt.js
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@ -205,7 +205,7 @@ function parse_hit(s, opt)
function bwa_postalt(args)
{
var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, update_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:0.8 };
var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, update_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:1 };
while ((c = getopt(args, 'Pqev:p:r:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg);
@ -225,13 +225,14 @@ function bwa_postalt(args)
if (args.length == getopt.ind) {
print("");
print("Usage: k8 bwa-postalt.js [options] <alt.sam> [aln.sam]\n");
print("Options: -p STR prefix of file(s) for additional information [null]");
print(" PREFIX.ctw - weight of each ALT contig");
print(" PREFIX.evi - reads supporting ALT contigs (effective with -e)");
print(" -q don't modify mapQ for non-ALTs hit overlapping lifted ALT");
print(" -e show reads supporting ALT contigs into file PREFIX.evi");
print("Options: -p STR prefix of file(s) for additional information [null]");
print(" PREFIX.ctw - weight of each ALT contig");
print(" PREFIX.evi - reads supporting ALT contigs (effective with -e)");
print(" -e show reads supporting ALT contigs into file PREFIX.evi");
print(" -r FLOAT reduce mapQ to 0 if not overlapping lifted best and pa<FLOAT ["+opt.min_pa_ratio+"]");
print(" -q don't modify mapQ for non-ALTs hit overlapping lifted ALT");
print("");
print("Note: This script inspects the XA tag, lifts the mapping positions of ALT hits to");
print("Note: This script extracts the XA tag, lifts the mapping positions of ALT hits to");
print(" the primary assembly, groups them and then estimates mapQ across groups. If");
print(" a non-ALT hit overlaps a lifted ALT hit, its mapping quality is set to the");
print(" smaller between its original mapQ and the adjusted mapQ of the ALT hit. If");