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don't call SNPs involving 'n'

This commit is contained in:
Heng Li 2018-02-09 13:27:17 -05:00
parent 8428809369
commit 42dab6319b
1 changed files with 6 additions and 2 deletions
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8
misc/paftools.js
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@ -286,8 +286,12 @@ function paf_call(args)
} else if (m[1] == '*') { } else if (m[1] == '*') {
if (rev) qs = y - 1, qe = y, --y; if (rev) qs = y - 1, qe = y, --y;
else qs = y, qe = y + 1, ++y; else qs = y, qe = y + 1, ++y;
out.push([t[5], x, x+1, cov, t[11], m[2].charAt(0), m[2].charAt(1), query, qs, qe, rev? '-' : '+']); var br = m[2].charAt(0), bq = m[2].charAt(1);
++x, ++blen, ++n_diff; if (br != 'n' && bq != 'n') { // don't call a SNP if there is an ambiguous base
out.push([t[5], x, x+1, cov, t[11], br, bq, query, qs, qe, rev? '-' : '+']);
++n_diff;
}
++x, ++blen;
} else if (m[1] == '+') { } else if (m[1] == '+') {
var l = m[2].length; var l = m[2].length;
if (rev) qs = y - l, qe = y, y -= l; if (rev) qs = y - l, qe = y, y -= l;