From 42dab6319bcad93a6421539ed419751b14e5f683 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 9 Feb 2018 13:27:17 -0500 Subject: [PATCH] don't call SNPs involving 'n' --- misc/paftools.js | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/misc/paftools.js b/misc/paftools.js index 9d7ea38..eada465 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -286,8 +286,12 @@ function paf_call(args) } else if (m[1] == '*') { if (rev) qs = y - 1, qe = y, --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? '-' : '+']); - ++x, ++blen, ++n_diff; + var br = m[2].charAt(0), bq = m[2].charAt(1); + 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] == '+') { var l = m[2].length; if (rev) qs = y - l, qe = y, y -= l;