[med-svn] samtools 21/26: Usage message tweaks to satisfy test/test.pl's test_usage()

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit d141b26ab788fc7abc33e0701bfdfb52c24094c0
Author: John Marshall <jm18 at sanger.ac.uk>
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);

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