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r745: junceval - recognize "-" as file name

This commit is contained in:
Heng Li 2018-03-15 12:48:33 -04:00
parent 7a0c1316ce
commit 242ff4e91d
1 changed files with 4 additions and 4 deletions
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8
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = 'r743';
var paftools_version = 'r746';
/*****************************
***** Library functions *****
@ -1758,7 +1758,7 @@ function paf_junceval(args)
else if (c == 'p') print_ovlp = true;
}
if (args.length - getopt.ind < 2) {
if (args.length - getopt.ind < 1) {
print("Usage: paftools.js junceval [options] <gene.gtf> <aln.sam>");
print("Options:");
print(" -l INT tolerance of junction positions (0 for exact) [0]");
@ -1770,7 +1770,7 @@ function paf_junceval(args)
var file, buf = new Bytes();
var tr = {};
file = new File(args[getopt.ind]);
file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0].charAt(0) == '#') continue;
@ -1815,7 +1815,7 @@ function paf_junceval(args)
var n_pri = 0, n_unmapped = 0, n_mapped = 0;
var n_sgl = 0, n_splice = 0, n_splice_hit = 0, n_splice_novel = 0;
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 re_cigar = /(\d+)([MIDNSHX=])/g;
while (file.readline(buf) >= 0) {