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r1141: junceval to support miniprot output

This commit is contained in:
Heng Li 2022-09-09 16:28:23 -04:00
parent 6252e5e367
commit fc6869a9e8
1 changed files with 41 additions and 10 deletions
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51
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.24-r1132-dirty'; var paftools_version = '2.24-r1141-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -2345,12 +2345,13 @@ function paf_pbsim2fq(args)
function paf_junceval(args) function paf_junceval(args)
{ {
var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false; var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false;
while ((c = getopt(args, "l:epc")) != null) { while ((c = getopt(args, "l:epca")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg); if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'e') print_err_only = print_ovlp = true; else if (c == 'e') print_err_only = print_ovlp = true;
else if (c == 'p') print_ovlp = true; else if (c == 'p') print_ovlp = true;
else if (c == 'c') chr_only = true; else if (c == 'c') chr_only = true;
else if (c == 'a') aa = true;
} }
if (args.length - getopt.ind < 1) { if (args.length - getopt.ind < 1) {
@ -2360,6 +2361,7 @@ function paf_junceval(args)
print(" -p print overlapping introns"); print(" -p print overlapping introns");
print(" -e print erroreous overlapping introns"); print(" -e print erroreous overlapping introns");
print(" -c only consider alignments to /^(chr)?([0-9]+|X|Y)$/"); print(" -c only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
print(" -a miniprot PAF");
exit(1); exit(1);
} }
@ -2413,7 +2415,7 @@ function paf_junceval(args)
file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]); file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]);
var last_qname = null; var last_qname = null;
var re_cigar = /(\d+)([MIDNSHP=X])/g; var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g;
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t"); var m, t = buf.toString().split("\t");
var ctg_name = null, cigar = null, pos = null, qname = t[0]; var ctg_name = null, cigar = null, pos = null, qname = t[0];
@ -2449,12 +2451,41 @@ function paf_junceval(args)
} }
var intron = []; var intron = [];
while ((m = re_cigar.exec(cigar)) != null) { if (aa) {
var len = parseInt(m[1]), op = m[2]; var tmp_junc = [], tmp = 0;
if (op == 'N') { while ((m = re_cigar.exec(cigar)) != null) {
intron.push([pos, pos + len]); var len = parseInt(m[1]), op = m[2];
pos += len; if (op == 'N') {
} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len; tmp_junc.push([tmp, tmp + len]);
tmp += len;
} else if (op == 'U') {
tmp_junc.push([tmp + 1, tmp + len - 2]);
tmp += len;
} else if (op == 'V') {
tmp_junc.push([tmp + 2, tmp + len - 1]);
tmp += len;
} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') {
tmp += len * 3;
} else if (op == 'F' || op == 'G') {
tmp += len;
}
}
if (t[4] == '+') {
for (var i = 0; i < tmp_junc.length; ++i)
intron.push([pos + tmp_junc[i][0], pos + tmp_junc[i][1]]);
} else if (t[4] == '-') {
var glen = parseInt(t[8]) - parseInt(t[7]);
for (var i = tmp_junc.length - 1; i >= 0; --i)
intron.push([pos + (glen - tmp_junc[i][1]), pos + (glen - tmp_junc[i][0])]);
}
} else {
while ((m = re_cigar.exec(cigar)) != null) {
var len = parseInt(m[1]), op = m[2];
if (op == 'N') {
intron.push([pos, pos + len]);
pos += len;
} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
}
} }
if (intron.length == 0) { if (intron.length == 0) {
++n_sgl; ++n_sgl;