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rework misc/README; progressing but unfinished

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This commit is contained in:
Heng Li
2018-02-12 22:06:05 -05:00
parent 7ef5490884
commit 874b8c4795
2 changed files with 55 additions and 69 deletions
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misc/paftools.js
+3 -3
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@@ -175,7 +175,7 @@ function paf_liftover(args)
{
if (fn == null) return null;
if (typeof to_merge == 'undefined') to_merge = true;
var file = new File(fn);
var file = fn == '-'? new File() : new File(fn);
var buf = new Bytes();
var bed = {};
while (file.readline(buf) >= 0) {
@@ -214,7 +214,7 @@ function paf_liftover(args)
}
var bed = read_bed(args[getopt.ind+1], to_merge);
var file = new File(args[getopt.ind]);
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
var buf = new Bytes();
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
@@ -485,7 +485,7 @@ function paf_stat(args)
}
var buf = new Bytes();
var file = new File(args[getopt.ind]);
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
var re = /(\d+)([MIDSHNX=])/g;
var lineno = 0, n_pri = 0, n_2nd = 0, n_seq = 0, n_cigar_64k = 0, l_tot = 0, l_cov = 0;