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r697: fixed wrong #mapped reads in junceval

This commit is contained in:
Heng Li 2018-02-09 18:45:57 -05:00
parent 6e65c5e631
commit 87cf650168
1 changed files with 7 additions and 3 deletions
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10
misc/paftools.js
View File

@ -1,5 +1,7 @@
#!/usr/bin/env k8
// Version: r697
/*****************************
***** Library functions *****
*****************************/
@ -1329,7 +1331,7 @@ function paf_pbsim2fq(args)
buf2.destroy();
}
function paf_junceval(args) // FIXME: the reported number of mapped reads is slightly off
function paf_junceval(args)
{
var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false;
while ((c = getopt(args, "l:ep")) != null) {
@ -1410,7 +1412,10 @@ function paf_junceval(args) // FIXME: the reported number of mapped reads is sli
continue;
} else {
++n_pri;
if (last_qname != t[0]) ++n_mapped;
if (last_qname != t[0]) {
++n_mapped;
last_qname = t[0];
}
}
var pos = parseInt(t[3]) - 1, intron = [];
@ -1462,7 +1467,6 @@ function paf_junceval(args) // FIXME: the reported number of mapped reads is sli
} else {
n_splice_novel += intron.length;
}
last_qname = t[0];
}
file.close();