From 9f728dd96a00abdc53cdf8b67b363e110bdcae49 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 26 Jul 2017 18:30:29 -0400 Subject: [PATCH] tunable overlap ratio --- misc/pbsim-eval.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/misc/pbsim-eval.js b/misc/pbsim-eval.js index 0e45429..971ba25 100644 --- a/misc/pbsim-eval.js +++ b/misc/pbsim-eval.js @@ -36,9 +36,10 @@ var getopt = function(args, ostr) { return optopt; } -var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false; -while ((c = getopt(arguments, "Q:")) != null) { +var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.333; +while ((c = getopt(arguments, "Q:r:")) != null) { if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true; + else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg); } var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]); @@ -61,7 +62,7 @@ function is_correct(s, b) o = (s[2] < b[2]? s[2] : b[2]) - s[1]; l = (s[2] > b[2]? s[2] : b[2]) - b[1]; } - return o/l > .333? true : false; + return o/l > ovlp_ratio? true : false; } function count_err(qname, a, tot, err, mode)