From a4c93e9377a8a47d77228a827d4f9cfe50689766 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 12 Oct 2024 23:31:17 -0400 Subject: [PATCH] support X and = in mapeval --- misc/paftools.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/misc/paftools.js b/misc/paftools.js index 3bd95ff..bfc9960 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -2187,7 +2187,7 @@ function paf_mapeval(args) } 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) { var m, line = buf.toString(); ++lineno; @@ -2225,7 +2225,7 @@ function paf_mapeval(args) var n_gap = 0, mlen = 0; while ((m = re_cigar.exec(t[5])) != null) { 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] == 'D') n_gap += len, pos_end += len; }