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a bit code cleanup

This commit is contained in:
Heng Li 2014-11-04 14:30:31 -05:00
parent 96fba0f2f4
commit 12fff1ad57
1 changed files with 8 additions and 10 deletions
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18
bwa-typeHLA.js
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@ -97,7 +97,6 @@ while (file.readline(buf) >= 0) {
else if (m[2] == 'D') te += l; else if (m[2] == 'D') te += l;
else if (m[2] == 'S' || m[2] == 'H') clip[x==0?0:1] = l; else if (m[2] == 'S' || m[2] == 'H') clip[x==0?0:1] = l;
} }
//if (x < min_qal && clip[0] + clip[1] > 0) continue;
var tl = len[t[2]]; var tl = len[t[2]];
var left = ts < clip[0]? ts : clip[0]; var left = ts < clip[0]? ts : clip[0];
var right = tl - te < clip[1]? tl - te : clip[1]; var right = tl - te < clip[1]? tl - te : clip[1];
@ -179,20 +178,19 @@ for (var e = 0; e < exons.length; ++e) {
var named_ca = []; var named_ca = [];
for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]); for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]);
warn("Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])..."); warn("Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
// convert representation again // set unmapped entries to high mismatch
var sc = []; var sc = [];
for (var k = 0; k < ga.length; ++k) {
var g = ga[k];
if (sc[g] == null) sc[g] = [];
for (var i = 0; i < ca.length; ++i)
sc[g][ca[i]] = 0xff;
}
// convert representation again
for (var i = 0; i < ee.length; ++i) { for (var i = 0; i < ee.length; ++i) {
var c = ee[i][0], g = ee[i][1]; var c = ee[i][0], g = ee[i][1];
if (sc[g] == null) sc[g] = [];
if (sc[g][c] == null) sc[g][c] = 0xffff;
sc[g][c] = sc[g][c] < ee[i][2]? sc[g][c] : ee[i][2]; sc[g][c] = sc[g][c] < ee[i][2]? sc[g][c] : ee[i][2];
} }
// set unmapped entries to high mismatch
for (var i = 0; i < ga.length; ++i)
for (var j = 0; j < ca.length; ++j) {
var g = ga[i], c = ca[j];
if (sc[g][c] == null) sc[g][c] = 0xff;
}
// drop mismapped contigs // drop mismapped contigs
var dropped = []; var dropped = [];
for (var k = 0; k < ca.length; ++k) { for (var k = 0; k < ca.length; ++k) {