From ad18fa490d61990ee01814afb246682ddaecc276 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 30 Jan 2018 10:11:50 -0500 Subject: [PATCH] fixed typos --- misc/paf2diff.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/misc/paf2diff.js b/misc/paf2diff.js index cc96dd1..30fdd28 100644 --- a/misc/paf2diff.js +++ b/misc/paf2diff.js @@ -40,9 +40,9 @@ var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g; var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, min_mapq = 5; while ((c = getopt(arguments, "l:L:g:q:")) != null) { if (c == 'l') min_cov_len = parseInt(getopt.arg); - else if (c == 'L') min_var_len = parseInt(optarg.arg); - else if (c == 'g') gap_thres = parseInt(optarg.arg); - else if (c == 'q') min_mapq = parseInt(optarg.arg); + else if (c == 'L') min_var_len = parseInt(getopt.arg); + else if (c == 'g') gap_thres = parseInt(getopt.arg); + else if (c == 'q') min_mapq = parseInt(getopt.arg); } if (arguments.length == getopt.ind) { @@ -55,7 +55,7 @@ if (arguments.length == getopt.ind) { exit(1); } -var file = new File(arguments[getopt.ind]); +var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]); var buf = new Bytes(); var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0], n_del = [0, 0, 0, 0];