From 98d794938b2ebe8cabe32fde7b0519007e54699d Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 24 Mar 2009 10:36:38 +0000 Subject: [PATCH] * samtools-0.1.2-17 * incorporating Nils' changes * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils) --- Makefile => Makefile.std | 0 bam_sort.c | 2 +- bam_tview.c | 1 + bamtk.c | 2 +- misc/{Makefile => Makefile.std} | 0 samtools.1 | 10 ++++++++-- 6 files changed, 11 insertions(+), 4 deletions(-) rename Makefile => Makefile.std (100%) rename misc/{Makefile => Makefile.std} (100%) diff --git a/Makefile b/Makefile.std similarity index 100% rename from Makefile rename to Makefile.std diff --git a/bam_sort.c b/bam_sort.c index f089cdf..dbe7495 100644 --- a/bam_sort.c +++ b/bam_sort.c @@ -221,7 +221,7 @@ int bam_sort(int argc, char *argv[]) } } if (optind + 2 > argc) { - fprintf(stderr, "Usage: samtools sort [-n] [-m ] \n"); + fprintf(stderr, "Usage: samtools sort [-n] [-m ] \n"); return 1; } bam_sort_core(is_by_qname, argv[optind], argv[optind+1], max_mem); diff --git a/bam_tview.c b/bam_tview.c index e71a386..77d60a0 100644 --- a/bam_tview.c +++ b/bam_tview.c @@ -257,6 +257,7 @@ void tv_loop(tview_t *tv) tid = tv->curr_tid; pos = tv->left_pos; while (1) { int c = getch(); + if(256 < c) {c = 1 + (c%256);} // Terminal was displaying ctrl-H as 263 via ssh from Mac OS X 10.5 computer switch (c) { case '?': tv_win_help(tv); break; case '\033': diff --git a/bamtk.c b/bamtk.c index be37b63..6f0ff99 100644 --- a/bamtk.c +++ b/bamtk.c @@ -3,7 +3,7 @@ #include "bam.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.2-16" +#define PACKAGE_VERSION "0.1.2-17" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/misc/Makefile b/misc/Makefile.std similarity index 100% rename from misc/Makefile rename to misc/Makefile.std diff --git a/samtools.1 b/samtools.1 index 1bf96e6..6b1879a 100644 --- a/samtools.1 +++ b/samtools.1 @@ -96,7 +96,7 @@ will be created. .TP .B view -samtools view [-b] [region1 [...]] +samtools view [-bhH] [region1 [...]] Extract/print all or sub alignments in SAM or BAM format. If no region is specified, all the alignments will be printed; otherwise only @@ -110,6 +110,12 @@ format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. .TP 8 .B -b Output in the BAM format. +.TP +.B -h +Include the header in the output. +.TP +.B -H +Output the header only. .RE .TP @@ -203,7 +209,7 @@ as in the default format we may not know the mapping quality. .TP .B -c -Call the consensus sequnce using MAQ consensus model. Options +Call the consensus sequence using MAQ consensus model. Options .B -T, .B -N and -- 2.39.2