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code backup

This commit is contained in:
Heng Li 2014-05-06 11:57:02 -04:00
parent 024195db62
commit 8d37726325
1 changed files with 13 additions and 7 deletions
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20
bwa-helper.js
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@ -519,8 +519,8 @@ function bwa_genalt(args)
var phits = []; var phits = [];
for (var i = 0; i < hits.length; ++i) { for (var i = 0; i < hits.length; ++i) {
var h = hits[i]; var h = hits[i];
if (h.length > 7) phits.push([h[7], h[9], h[10], -1]); // lifted if (h.length > 7) phits.push([h[7], h[9], h[10], -1, i]); // lifted
else phits.push([h[0], h[2], h[3], -1]); else phits.push([h[0], h[2], h[3], -1, i]);
} }
phits.sort(function(a,b) { phits.sort(function(a,b) {
if (a[0] != b[0]) return a[0] < b[0]? -1 : 1; if (a[0] != b[0]) return a[0] < b[0]? -1 : 1;
@ -539,9 +539,12 @@ function bwa_genalt(args)
end = end > phits[i][2]? end : phits[i][2]; end = end > phits[i][2]? end : phits[i][2];
} }
} }
var reported_groupid = null;
for (var i = 0; i < phits.length; ++i)
if (phits[i][4] == 0) reported_groupid = phits[i][3];
var n_group0 = 0; // #hits overlapping the reported hit var n_group0 = 0; // #hits overlapping the reported hit
for (var i = 0; i < phits.length; ++i) for (var i = 0; i < phits.length; ++i)
if (phits[i][3] == phits[0][3]) if (phits[i][3] == phits[reported_groupid][3])
++n_group0; ++n_group0;
if (n_group0 == 1) { // then keep the reported alignment and mapQ if (n_group0 == 1) { // then keep the reported alignment and mapQ
//print(line); //print(line);
@ -551,21 +554,24 @@ function bwa_genalt(args)
// re-estimate mapQ // re-estimate mapQ
var group_max = []; var group_max = [];
for (var i = 0; i < phits.length; ++i) for (var i = 0; i < phits.length; ++i)
if (group_max[phits[i][3]] == null || group_max[phits[i][3]][0] < hits[i][6]) if (group_max[phits[i][3]] == null || group_max[phits[i][3]][0] < hits[phits[i][4]][6])
group_max[phits[i][3]] = [hits[i][6], phits[i][3]]; group_max[phits[i][3]] = [hits[phits[i][4]][6], phits[i][3]];
if (group_max.length > 1) if (group_max.length > 1)
group_max.sort(function(x,y) {return y[0]-x[0]}); group_max.sort(function(x,y) {return y[0]-x[0]});
var mapQ; var mapQ;
if (group_max[0][1] == phits[0][3]) { // the best hit is the hit reported in SAM if (group_max[0][1] == reported_groupid) { // the best hit is the hit reported in SAM
mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]); mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
} else mapQ = 0; } else mapQ = 0;
mapQ = mapQ < 60? mapQ : 60; mapQ = mapQ < 60? mapQ : 60;
var ori_mapQ = parseInt(t[4]); var ori_mapQ = parseInt(t[4]);
mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ; mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
// print
t[4] = mapQ; t[4] = mapQ;
print(t.join("\t")); print(t.join("\t"));
print("*", mapQ); for (var i = 0; i < phits.length; ++i) {
}
print("*", mapQ, ori_mapQ);
for (var i = 0; i < hits.length; ++i) for (var i = 0; i < hits.length; ++i)
print(hits[i]); print(hits[i]);
} }