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use weight1 by default

This commit is contained in:
Heng Li 2014-10-14 14:50:37 -04:00
parent df20911110
commit 15becdd3df
1 changed files with 5 additions and 5 deletions
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10
bwa-postalt.js
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@ -205,14 +205,14 @@ 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, recover_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:100, show_ev:false, wei1:false }; var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, recover_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:100, show_ev:false, wei1:true };
while ((c = getopt(args, '1pqev:')) != null) { while ((c = getopt(args, 'wpqev:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg); if (c == 'v') opt.verbose = parseInt(getopt.arg);
else if (c == 'p') opt.show_pri = true; else if (c == 'p') opt.show_pri = true;
else if (c == 'q') opt.recover_maq = false; else if (c == 'q') opt.recover_maq = false;
else if (c == 'e') opt.show_ev = true; else if (c == 'e') opt.show_ev = true;
else if (c == '1') opt.wei1 = true; else if (c == 'w') opt.wei1 = false;
} }
if (args.length == getopt.ind) { if (args.length == getopt.ind) {
@ -434,9 +434,9 @@ function bwa_postalt(args)
for (var i = 0; i < hits2.length; ++i) for (var i = 0; i < hits2.length; ++i)
if (weight_alt[hits2[i][3]] != null) if (weight_alt[hits2[i][3]] != null)
alts[hits2[i][3]] = [hits2[i][4], hits2[i][5]]; alts[hits2[i][3]] = [hits2[i][4], hits2[i][5]];
if (idx_pri[hits2[0][0]] != null) { if (idx_pri[hits2[0][0]] != null) { // add other unreported hits
var ovlp = idx_pri[hits2[0][0]](start, end); var ovlp = idx_pri[hits2[0][0]](start, end);
for (var i = 0; i < ovlp.length; ++i) // TODO: requiring reasonable overlap for (var i = 0; i < ovlp.length; ++i)
if (ovlp[i][0] <= start && end <= ovlp[i][1] && alts[ovlp[i][2]] == null) if (ovlp[i][0] <= start && end <= ovlp[i][1] && alts[ovlp[i][2]] == null)
alts[ovlp[i][2]] = [0, 0]; alts[ovlp[i][2]] = [0, 0];
} }