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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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7
bwa-postalt.js
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@ -205,7 +205,7 @@ function parse_hit(s, opt)
function bwa_postalt(args) 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) { while ((c = getopt(args, 'Pqev:p:r:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg); if (c == 'v') opt.verbose = parseInt(getopt.arg);
@ -228,10 +228,11 @@ function bwa_postalt(args)
print("Options: -p STR prefix of file(s) for additional information [null]"); print("Options: -p STR prefix of file(s) for additional information [null]");
print(" PREFIX.ctw - weight of each ALT contig"); print(" PREFIX.ctw - weight of each ALT contig");
print(" PREFIX.evi - reads supporting ALT contigs (effective with -e)"); 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(" -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("");
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(" 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(" 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"); print(" smaller between its original mapQ and the adjusted mapQ of the ALT hit. If");