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code backup

This commit is contained in:
Heng Li 2014-10-20 14:17:56 -04:00
parent 6f41a27e27
commit 25d45512d9
2 changed files with 8 additions and 7 deletions
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13
bwa-postalt.js
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@ -207,13 +207,13 @@ 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: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, recover_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:0.8 };
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);
else if (c == 'p') opt.pre = getopt.arg; else if (c == 'p') opt.pre = 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 == 'r') opt.min_pa_ratio = parseFloat(optarg.arg); else if (c == 'r') opt.min_pa_ratio = parseFloat(getopt.arg);
} }
if (opt.min_pa_ratio > 1.) opt.min_pa_ratio = 1.; if (opt.min_pa_ratio > 1.) opt.min_pa_ratio = 1.;
@ -485,20 +485,21 @@ function bwa_postalt(args)
if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) { if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) {
var l = rpt_lifted; var l = rpt_lifted;
for (var i = 0; i < buf2.length; ++i) { for (var i = 0; i < buf2.length; ++i) {
var s = buf2[i]; var s = buf2[i], is_ovlp = true;
if (l[0] != s[2]) continue; // different chr if (l[0] != s[2]) is_ovlp = false; // different chr
if (((s[1]&16) != 0) != l[1]) continue; // different strand if (((s[1]&16) != 0) != l[1]) is_ovlp = false; // different strand
var start = s[3] - 1, end = start; var start = s[3] - 1, end = start;
while ((m = re_cigar.exec(t[5])) != null) while ((m = re_cigar.exec(t[5])) != null)
if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N') if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
end += parseInt(m[1]); end += parseInt(m[1]);
if (!(start < l[3] && l[2] < end)) is_ovlp = false; // no overlap
var om = -1, pa = 10.; var om = -1, pa = 10.;
for (var j = 11; j < s.length; ++j) for (var j = 11; j < s.length; ++j)
if ((m = /^om:i:(\d+)/.exec(s[j])) != null) if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
om = parseInt(m[1]); om = parseInt(m[1]);
else if ((m = /^pa:f:(\S+)/.exec(s[j])) != null) else if ((m = /^pa:f:(\S+)/.exec(s[j])) != null)
pa = parseFloat(m[1]); pa = parseFloat(m[1]);
if (start < l[3] && l[2] < end) { // overlapping the lifted hit if (is_ovlp) { // overlapping the lifted hit
if (om > 0) s[4] = om; if (om > 0) s[4] = om;
s[4] = s[4] < mapQ? s[4] : mapQ; s[4] = s[4] < mapQ? s[4] : mapQ;
} else if (pa < opt.min_pa_ratio) { // not overlapping; has a small pa } else if (pa < opt.min_pa_ratio) { // not overlapping; has a small pa

2
bwt.c
View File

@ -305,10 +305,10 @@ int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv,
if (q[i] < 4) { // an A/C/G/T base if (q[i] < 4) { // an A/C/G/T base
c = 3 - q[i]; // complement of q[i] c = 3 - q[i]; // complement of q[i]
bwt_extend(bwt, &ik, ok, 0); bwt_extend(bwt, &ik, ok, 0);
if (ik.x[2] < max_intv && (i - x > max_len || ik.x[2] == 1)) break;
if (ok[c].x[2] != ik.x[2]) { // change of the interval size if (ok[c].x[2] != ik.x[2]) { // change of the interval size
kv_push(bwtintv_t, *curr, ik); kv_push(bwtintv_t, *curr, ik);
if (ok[c].x[2] < min_intv) break; // the interval size is too small to be extended further if (ok[c].x[2] < min_intv) break; // the interval size is too small to be extended further
if (i - x > max_len && ik.x[2] < max_intv) break;
} }
ik = ok[c]; ik.info = i + 1; ik = ok[c]; ik.info = i + 1;
} else { // an ambiguous base } else { // an ambiguous base