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support X and = in mapeval

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Heng Li
2024-10-12 23:31:17 -04:00
parent 7d69334e69
commit a4c93e9377
1 changed files with 2 additions and 2 deletions
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misc/paftools.js
+2 -2
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@@ -2187,7 +2187,7 @@ function paf_mapeval(args)
} }
var lineno = 0, last = null, a = [], n_unmapped = null; var lineno = 0, last = null, a = [], n_unmapped = null;
var re_cigar = /(\d+)([MIDSHN])/g; var re_cigar = /(\d+)([MIDSHN=X])/g;
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var m, line = buf.toString(); var m, line = buf.toString();
++lineno; ++lineno;
@@ -2225,7 +2225,7 @@ function paf_mapeval(args)
var n_gap = 0, mlen = 0; var n_gap = 0, mlen = 0;
while ((m = re_cigar.exec(t[5])) != null) { while ((m = re_cigar.exec(t[5])) != null) {
var len = parseInt(m[1]); var len = parseInt(m[1]);
if (m[2] == 'M') pos_end += len, mlen += len; if (m[2] == 'M' || m[2] == 'X' || m[2] == '=') pos_end += len, mlen += len;
else if (m[2] == 'I') n_gap += len; else if (m[2] == 'I') n_gap += len;
else if (m[2] == 'D') n_gap += len, pos_end += len; else if (m[2] == 'D') n_gap += len, pos_end += len;
} }