From 362fd7d8382030e450c0849b7ce8ac30eba2525b Mon Sep 17 00:00:00 2001 From: Mingfu Shao Date: Thu, 16 Sep 2021 07:54:08 +0000 Subject: [PATCH] update cmd --- src/config.cc | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/config.cc b/src/config.cc index aa84a1c..c150cd4 100644 --- a/src/config.cc +++ b/src/config.cc @@ -378,6 +378,11 @@ int parse_arguments(int argc, const char ** argv) verbose = atoi(argv[i + 1]); i++; } + else if(string(argv[i]) == "--assemble_duplicates") + { + assemble_duplicates = atoi(argv[i + 1]); + i++; + } else if(string(argv[i]) == "--batch_bundle_size") { batch_bundle_size = atoi(argv[i + 1]); @@ -541,6 +546,7 @@ int print_help() printf(" %-42s %s\n", "--version", "print current version of Scallop and exit"); printf(" %-42s %s\n", "--preview", "determine fragment-length-range and library-type and exit"); printf(" %-42s %s\n", "--verbose <0, 1, 2>", "0: quiet; 1: one line for each graph; 2: with details, default: 1"); + printf(" %-42s %s\n", "--assemble_duplicates ", "the number of consensus runs of the decomposition, default: 10"); printf(" %-42s %s\n", "--library_type ", "library type of the sample, default: unstranded"); printf(" %-42s %s\n", "--min_transcript_coverage ", "minimum coverage required for a multi-exon transcript, default: 0.5"); printf(" %-42s %s\n", "--min_single_exon_coverage ", "minimum coverage required for a single-exon transcript, default: 20");