This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit d141b26ab788fc7abc33e0701bfdfb52c24094c0 Author: John Marshall <[email protected]> Date: Wed Dec 4 17:04:22 2013 +0000 Usage message tweaks to satisfy test/test.pl's test_usage() Idxstats is currently disabled, but re-enable its basic functionality including usage. The calmd/fillmd command is canonically calmd. Fix bamshuf and faidx messages. Tview has been disabled in bamtk.c for a while; also suppress it in samtools --help command listing. --- bam_index.c | 4 +++- bam_md.c | 2 +- bamshuf.c | 2 +- bamtk.c | 2 +- faidx.c | 2 +- 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/bam_index.c b/bam_index.c index 3858b2e..c78e030 100644 --- a/bam_index.c +++ b/bam_index.c @@ -19,11 +19,12 @@ int bam_index(int argc, char *argv[]) int bam_idxstats(int argc, char *argv[]) { -#if 0 bam_index_t *idx; bam_header_t *header; bamFile fp; +#if 0 int i; +#endif if (argc < 2) { fprintf(stderr, "Usage: samtools idxstats <in.bam>\n"); return 1; @@ -34,6 +35,7 @@ int bam_idxstats(int argc, char *argv[]) bam_close(fp); idx = bam_index_load(argv[1]); if (idx == 0) { fprintf(stderr, "[%s] fail to load the index.\n", __func__); return 1; } +#if 0 for (i = 0; i < idx->n; ++i) { khint_t k; khash_t(i) *h = idx->index[i]; diff --git a/bam_md.c b/bam_md.c index 7656bd1..8e58c36 100644 --- a/bam_md.c +++ b/bam_md.c @@ -341,7 +341,7 @@ int bam_fillmd(int argc, char *argv[]) if (is_uncompressed) strcat(mode_w, "u"); if (optind + 1 >= argc) { fprintf(stderr, "\n"); - fprintf(stderr, "Usage: samtools fillmd [-eubrS] <aln.bam> <ref.fasta>\n\n"); + fprintf(stderr, "Usage: samtools calmd [-eubrS] <aln.bam> <ref.fasta>\n\n"); fprintf(stderr, "Options: -e change identical bases to '='\n"); fprintf(stderr, " -u uncompressed BAM output (for piping)\n"); fprintf(stderr, " -b compressed BAM output\n"); diff --git a/bamshuf.c b/bamshuf.c index 11ca415..75900ba 100644 --- a/bamshuf.c +++ b/bamshuf.c @@ -129,7 +129,7 @@ int main_bamshuf(int argc, char *argv[]) } if (is_un) clevel = 0; if (optind + 2 > argc) { - fprintf(stderr, "\nUsage: bamshuf [-Ou] [-n nFiles] [-c cLevel] <in.bam> <out.prefix>\n\n"); + fprintf(stderr, "\nUsage: samtools bamshuf [-Ou] [-n nFiles] [-c cLevel] <in.bam> <out.prefix>\n\n"); fprintf(stderr, "Options: -O output to stdout\n"); fprintf(stderr, " -u uncompressed BAM output\n"); fprintf(stderr, " -l INT compression level [%d]\n", DEF_CLEVEL); diff --git a/bamtk.c b/bamtk.c index 9c0dbe7..488f385 100644 --- a/bamtk.c +++ b/bamtk.c @@ -73,7 +73,7 @@ static void usage(FILE *fp) " stats generate stats (former bamcheck)\n" " -- viewing\n" " flags explain BAM flags\n" -" tview text alignment viewer\n" +//" tview text alignment viewer\n" " view SAM<->BAM conversion\n" //" depad convert padded BAM to unpadded BAM\n" // not stable "\n"); diff --git a/faidx.c b/faidx.c index 644be5d..9f24e00 100644 --- a/faidx.c +++ b/faidx.c @@ -19,7 +19,7 @@ static void error(const char *format, ...) else { fprintf(stderr, "\n"); - fprintf(stderr, "Usage: faidx <file.fa|file.fa.gz> [<reg> [...]]\n"); + fprintf(stderr, "Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]]\n"); fprintf(stderr, "\n"); } exit(-1); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
