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[pull] master from lh3:master #139

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Merged
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May 18, 2025
Merged

[pull] master from lh3:master #139

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9 changes: 8 additions & 1 deletion misc/paftools.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2613,7 +2613,8 @@ function paf_junceval(args)
function paf_exoneval(args) // adapted from paf_junceval()
{
var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false, is_bed = false, use_cds = false, eval_base = false;
while ((c = getopt(args, "l:epcab1ds")) != null) {
var skip_start = false, skip_last = false;
while ((c = getopt(args, "l:epcab1dsft")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'e') print_err_only = print_ovlp = true;
else if (c == 'p') print_ovlp = true;
Expand All @@ -2623,6 +2624,8 @@ function paf_exoneval(args) // adapted from paf_junceval()
else if (c == '1') first_only = true;
else if (c == 'd') use_cds = true;
else if (c == 's') eval_base = true;
else if (c == 'f') skip_start = true;
else if (c == 't') skip_last = skip_start = true;
}

if (args.length - getopt.ind < 1) {
Expand All @@ -2635,6 +2638,8 @@ function paf_exoneval(args) // adapted from paf_junceval()
print(" -e print erroreous overlapping exons");
print(" -c only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
print(" -1 only process the first alignment of each query");
print(" -f skip the first exon in the miniprot mode");
print(" -t skip the first and the last exons");
print(" -b BED as input");
print(" -s compute base Sn and Sp (more memory)");
exit(1);
Expand Down Expand Up @@ -2764,6 +2769,8 @@ function paf_exoneval(args) // adapted from paf_junceval()
for (var i = tmp_exon.length - 1; i >= 0; --i)
exon.push([pos + (glen - tmp_exon[i][1]), pos + (glen - tmp_exon[i][0])]);
}
if (skip_start) exon.shift();
if (skip_last) exon.pop();
} else {
var tmp_st = pos;
while ((m = re_cigar.exec(cigar)) != null) {
Expand Down
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