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output the number of mismatches

This commit is contained in:
Heng Li 2021-08-04 17:05:06 -04:00
parent 7e33fde82b
commit 629c11728e
1 changed files with 13 additions and 2 deletions
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15
misc/paftools.js
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@ -977,7 +977,7 @@ function paf_stat(args)
var re = /(\d+)([MIDSHNX=])/g;
var lineno = 0, n_pri = 0, n_2nd = 0, n_seq = 0, n_cigar_64k = 0, l_tot = 0, l_cov = 0;
var n_gap = [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]];
var n_gap = [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]], n_sub = 0;
function cov_len(regs)
{
@ -999,7 +999,7 @@ function paf_stat(args)
if (line.charAt(0) != '@') {
var t = line.split("\t", 12);
var m, rs, cigar = null, is_pri = false, is_sam = false, is_rev = false, tname = null;
var atlen = null, aqlen, qs, qe, mapq, ori_qlen, NM = null;
var atlen = null, aqlen, qs, qe, mapq, ori_qlen, NM = null, nn = 0;
if (t.length < 2) continue;
if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
if (t[4] == '*') continue; // unmapped
@ -1009,6 +1009,8 @@ function paf_stat(args)
}
if ((m = /\tNM:i:(\d+)/.exec(line)) != null)
NM = parseInt(m[1]);
if ((m = /\tnn:i:(\d+)/.exec(line)) != null)
nn = parseInt(m[1]);
if ((m = /\tcg:Z:(\S+)/.exec(line)) != null)
cigar = m[1];
if (cigar == null) {
@ -1032,6 +1034,8 @@ function paf_stat(args)
}
if ((m = /\tNM:i:(\d+)/.exec(line)) != null)
NM = parseInt(m[1]);
if ((m = /\tnn:i:(\d+)/.exec(line)) != null)
nn = parseInt(m[1]);
cigar = t[5];
tname = t[2];
rs = parseInt(t[3]) - 1;
@ -1078,6 +1082,12 @@ function paf_stat(args)
clip[M == 0? 0 : 1] = l;
}
}
if (NM != null) {
var tmp = NM - n_gap_all - nn;
if (tmp < 0) warn("WARNING: NM is smaller than the number of gaps at line " + lineno);
if (tmp < 0) tmp = 0;
n_sub += tmp;
}
if (n_cigar > 65535) ++n_cigar_64k;
if (ql + sclip != aqlen)
warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno + " (" + (ql+sclip) + " != " + aqlen + ")");
@ -1112,6 +1122,7 @@ function paf_stat(args)
print("Number of primary alignments with >65535 CIGAR operations: " + n_cigar_64k);
print("Number of bases in mapped sequences: " + l_tot);
print("Number of mapped bases: " + l_cov);
print("Number of substitutions: " + n_sub);
print("Number of insertions in [0,50): " + n_gap[0][0]);
print("Number of insertions in [50,100): " + n_gap[0][1]);
print("Number of insertions in [100,300): " + n_gap[0][2]);