From f7271a7c2480ff0f8382b568cf5d678ca69487f3 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 6 Aug 2021 19:41:46 -0400 Subject: [PATCH] expose mapQ threshold to command line of pafcmp --- misc/paftools.js | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/misc/paftools.js b/misc/paftools.js index c2c9ec1..656ec38 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -2949,13 +2949,16 @@ function paf_vcfsel(args) function paf_pafcmp(args) { - var c, opt = { min_len:5000, min_mapq:5, min_ovlp:0.5 }; - while ((c = getopt(args, "c:")) != null) { + var c, opt = { min_len:5000, min_mapq:10, min_ovlp:0.5 }; + while ((c = getopt(args, "q:")) != null) { + if (c == 'q') opt.min_mapq = parseInt(opt.arg); } var buf = new Bytes(); if (args.length - getopt.ind < 2) { print("Usage: paftools.js pafcmp [options] "); + print("Options:"); + print(" -q INT min mapping quality [" + opt.min_mapq + "]"); return 1; }