script to collect alignment stats
This commit is contained in:
Heng Li
parent
4ee3202539
commit
2f11a63b22
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@ -0,0 +1,128 @@
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var buf = new Bytes();
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var file = arguments.length? new File(arguments[0]) : new File();
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var re = /(\d+)([MIDSHNX=])/g;
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var lineno = 0, n_pri = 0, n_2nd = 0, n_seq = 0, n_cigar_64k = 0, l_tot = 0, l_cov = 0;
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var n_gap = [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]];
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function cov_len(regs)
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{
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regs.sort(function(a,b) {return a[0]-b[0]});
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var st = regs[0][0], en = regs[0][1], l = 0;
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for (var i = 1; i < regs.length; ++i) {
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if (regs[i][0] < en)
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en = en > regs[i][1]? en : regs[i][1];
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else l += en - st, st = regs[i][0], en = regs[i][1];
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}
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l += en - st;
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return l;
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}
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var last = null, last_qlen = null, regs = [];
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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++lineno;
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if (line.charAt(0) != '@') {
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var t = line.split("\t", 12);
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var m, cigar = null, is_pri = false, is_sam = false, is_rev = false;
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var atlen = null, aqlen, qs, qe, mapq, ori_qlen;
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if (t[4] == '+' || t[4] == '-') { // PAF
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if (!/\ts2:i:\d+/.test(line)) {
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++n_2nd;
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continue;
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}
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if ((m = /\tcg:Z:(\S+)/.exec(line)) != null)
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cigar = m[1];
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if (cigar == null) {
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warn("WARNING: no CIGAR at line " + lineno);
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continue;
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}
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qs = parseInt(t[2]), qe = parseInt(t[3]);
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aqlen = qe - qs;
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atlen = parseInt(t[8]) - parseInt(t[7]);
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mapq = parseInt(t[11]);
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ori_qlen = parseInt(t[1]);
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} else { // SAM
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var flag = parseInt(t[1]);
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if (flag & 4) continue;
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if (flag & 0x100) {
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++n_2nd;
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continue;
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}
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cigar = t[5];
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rs = parseInt(t[3]) - 1;
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mapq = parseInt(t[4]);
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aqlen = t[9].length;
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is_sam = true;
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is_rev = !!(flag&0x10);
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}
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++n_pri;
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if (last != t[0]) {
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if (last != null) {
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l_tot += last_qlen;
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l_cov += cov_len(regs);
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}
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regs = [];
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++n_seq, last = t[0];
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}
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var M = 0, tl = 0, ql = 0, clip = [0, 0], n_cigar = 0, sclip = 0;
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while ((m = re.exec(cigar)) != null) {
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var l = parseInt(m[1]);
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++n_cigar;
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if (m[2] == 'M' || m[2] == '=' || m[2] == 'X') {
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tl += l, ql += l, M += l;
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} else if (m[2] == 'I' || m[2] == 'D') {
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var type;
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if (l < 50) type = 0;
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else if (l < 100) type = 1;
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else if (l < 300) type = 2;
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else if (l < 400) type = 3;
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else if (l < 1000) type = 4;
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else type = 5;
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if (m[2] == 'I') ql += l, ++n_gap[0][type];
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else tl += l, ++n_gap[1][type];
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} else if (m[2] == 'N') {
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tl += l;
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} else if (m[2] == 'S') {
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clip[M == 0? 0 : 1] = l, sclip += l;
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} else if (m[2] == 'H') {
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clip[M == 0? 0 : 1] = l;
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}
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}
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if (n_cigar > 65535) ++n_cigar_64k;
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if (ql + sclip != aqlen)
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warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno);
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if (atlen != null && atlen != tl)
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warn("WARNING: aligned reference length is inconsistent with CIGAR at line " + lineno);
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if (is_sam) {
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qs = clip[is_rev? 1 : 0], qe = qs + ql;
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ori_qlen = clip[0] + ql + clip[1];
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}
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regs.push([qs, qe]);
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last_qlen = ori_qlen;
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}
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}
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l_tot += last_qlen;
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l_cov += cov_len(regs);
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print("Number of mapped sequences: " + n_seq);
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print("Number of primary alignments: " + n_pri);
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print("Number of secondary alignments: " + n_2nd);
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print("Number of primary alignments with >65535 CIGAR operations: " + n_cigar_64k);
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print("Number of bases in mapped sequences: " + l_tot);
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print("Number of mapped bases: " + l_cov);
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print("Number of insertions in [0,50): " + n_gap[0][0]);
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print("Number of insertions in [50,100): " + n_gap[0][1]);
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print("Number of insertions in [100,300): " + n_gap[0][2]);
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print("Number of insertions in [300,400): " + n_gap[0][3]);
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print("Number of insertions in [400,1000): " + n_gap[0][4]);
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print("Number of insertions in [1000,inf): " + n_gap[0][5]);
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print("Number of deletions in [0,50): " + n_gap[1][0]);
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print("Number of deletions in [50,100): " + n_gap[1][1]);
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print("Number of deletions in [100,300): " + n_gap[1][2]);
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print("Number of deletions in [300,400): " + n_gap[1][3]);
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print("Number of deletions in [400,1000): " + n_gap[1][4]);
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print("Number of deletions in [1000,inf): " + n_gap[1][5]);
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file.close();
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buf.destroy();
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