zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

junceval for plain junction BED as input

This commit is contained in:
Heng Li 2022-09-10 23:18:08 -04:00
parent 315795eefd
commit 6ed7263670
1 changed files with 13 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
misc/paftools.js
View File

@ -2345,13 +2345,15 @@ 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, aa = false; var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false, is_bed = false;
while ((c = getopt(args, "l:epca")) != null) { while ((c = getopt(args, "l:epcab1")) != 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; else if (c == 'a') aa = true;
else if (c == 'b') is_bed = true;
else if (c == '1') first_only = true;
} }
if (args.length - getopt.ind < 1) { if (args.length - getopt.ind < 1) {
@ -2361,7 +2363,9 @@ 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"); print(" -a miniprot PAF as input");
print(" -b BED as input");
print(" -1 only process the first alignment of each query");
exit(1); exit(1);
} }
@ -2421,7 +2425,9 @@ function paf_junceval(args)
var ctg_name = null, cigar = null, pos = null, qname = t[0]; var ctg_name = null, cigar = null, pos = null, qname = t[0];
if (t[0].charAt(0) == '@') continue; if (t[0].charAt(0) == '@') continue;
if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF if (is_bed) {
ctg_name = t[0], pos = parseInt(t[1]), cigar == null;
} else if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
ctg_name = t[5], pos = parseInt(t[7]); ctg_name = t[5], pos = parseInt(t[7]);
var type = 'P'; var type = 'P';
for (i = 12; i < t.length; ++i) { for (i = 12; i < t.length; ++i) {
@ -2451,7 +2457,9 @@ function paf_junceval(args)
} }
var intron = []; var intron = [];
if (aa) { if (is_bed) {
intron.push([pos, parseInt(t[2])]);
} else if (aa) {
var tmp_junc = [], tmp = 0; var tmp_junc = [], tmp = 0;
while ((m = re_cigar.exec(cigar)) != null) { while ((m = re_cigar.exec(cigar)) != null) {
var len = parseInt(m[1]), op = m[2]; var len = parseInt(m[1]), op = m[2];