From 90fb0c1e3ea9d4ffb5a731587418899e26a72956 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Mon, 27 Oct 2014 09:40:23 +0100 Subject: [PATCH] Add --no-mixed and --no-discordant to the command line options listed with -h (these are actually just passed through). --- herd/main.c | 5 +++++ main.c | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/herd/main.c b/herd/main.c index ea44812..f6d0b73 100644 --- a/herd/main.c +++ b/herd/main.c @@ -72,6 +72,11 @@ void usage(char *prog) { in samtools. The default is 1, but this may need to be increased as\n\ you increase the number of alotted nodes.\n\ \n\ +--no-discordant Suppress discordant alignments. This is actually a bowtie2\n\ + option.\n\ +\n\ +--no-mixed Suppress singleton alignments. This is actually a bowtie2 option.\n\ +\n\ --unmapped Save unaligned reads to a file or files (as appropriate). This files\n\ will be placed in the same directory as the source fastq files,\n\ regardless of whether \"-o\" is used.\n\ diff --git a/main.c b/main.c index 4cea228..6c3cb71 100644 --- a/main.c +++ b/main.c @@ -40,6 +40,11 @@ void usage(char *prog) { maximum value for this parameter is whatever an unsigned long is on\n\ your system.\n\ \n\ +--no-discordant Suppress discordant alignments. This is actually a bowtie2\n\ + option.\n\ +\n\ +--no-mixed Suppress singleton alignments. This is actually a bowtie2 option.\n\ +\n\ --unmapped Save unaligned reads to a file or files (as appropriate).\n\ \n\ --genome-size Many of the bison tools need to read the genome into memory. By\n\