From 242ff4e91d84766519dfb389f9e48ac318986c3b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 15 Mar 2018 12:48:33 -0400 Subject: [PATCH] r745: junceval - recognize "-" as file name --- misc/paftools.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/misc/paftools.js b/misc/paftools.js index add795c..ea14db0 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -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] "); 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) {