usage displays for .vcf.gz only

- include note on main usage page about indexed/un-indexed VCF/BCF and streams

main.c

@@ -146,7 +146,11 @@ static void usage(FILE *fp)
         if ( cmds[i].func && cmds[i].help[0]!='-' ) fprintf(fp, "\t%-15s %s\n", cmds[i].alias, cmds[i].help);
         i++;
     }
-
+    fprintf(fp,"\n");
+    fprintf(fp,"Notes:  Most commands accept VCF, bgzipped VCF and BCF with filetype detected\n");
+    fprintf(fp,"        automatically even when streaming from a pipe. Indexed VCF and BCF\n");
+    fprintf(fp,"        will work in all situations. Un-indexed VCF and BCF and streams will\n");
+    fprintf(fp,"        work in most, but not all situations.\n");
     fprintf(fp,"\n");
 }
 

vcfannotate.c

@@ -732,7 +732,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Annotate and edit VCF/BCF files.\n");
-    fprintf(stderr, "Usage:   bcftools annotate [options] <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n");
+    fprintf(stderr, "Usage:   bcftools annotate [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "   -a, --annotations <file>       VCF file or tabix-indexed file with annotations: CHR\\tPOS[\\tVALUE]+\n");

vcfcall.c

@@ -339,12 +339,12 @@ void parse_novel_rate(args_t *args, const char *str)
 static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
-    fprintf(stderr, "About: SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.\n");
-    fprintf(stderr, "       This command replaces the former \"bcftools view\" caller. Some of the original\n");
-    fprintf(stderr, "       functionality has been temporarily lost in the process of transition to htslib,\n");
-    fprintf(stderr, "       but will be added back on popular demand. The original calling model can be\n");
-    fprintf(stderr, "       invoked with the -c option.\n");
-    fprintf(stderr, "Usage: bcftools call [options] <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n");
+    fprintf(stderr, "About:   SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.\n");
+    fprintf(stderr, "         This command replaces the former \"bcftools view\" caller. Some of the original\n");
+    fprintf(stderr, "         functionality has been temporarily lost in the process of transition to htslib,\n");
+    fprintf(stderr, "         but will be added back on popular demand. The original calling model can be\n");
+    fprintf(stderr, "         invoked with the -c option.\n");
+    fprintf(stderr, "Usage:   bcftools call [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "File format options:\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>     output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");

vcfconcat.c

@@ -443,7 +443,7 @@ static void usage(args_t *args)
     fprintf(stderr, "About:   Concatenate and/or combine overlapping VCF/BCF files split e.g. by chromosome\n");
     fprintf(stderr, "         or variant type. All source files must have the same sample columns appearing\n");
     fprintf(stderr, "         in the same order.\n");
-    fprintf(stderr, "Usage:   bcftools concat [options] <A.bcf>|<A.vcf>|<A.vcf.gz> [<B.bcf>|<B.vcf>|<B.vcf.gz> ...]\n");
+    fprintf(stderr, "Usage:   bcftools concat [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
 	fprintf(stderr, "   -a, --allow-overlaps           Combine overlapping files. Requires indexed files.\n");

vcffilter.c

@@ -279,7 +279,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Apply fixed-threshold filters.\n");
-    fprintf(stderr, "Usage:   bcftools filter [options] <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n");
+    fprintf(stderr, "Usage:   bcftools filter [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "    -e, --exclude <expr>          exclude sites for which the expression is true (e.g. '%%TYPE=\"snp\" && %%QUAL>=10 && (DP4[2]+DP4[3] > 2')\n");

vcfgtcheck.c

@@ -652,8 +652,8 @@ static char *init_prefix(char *prefix)
 static void usage(void)
 {
     fprintf(stderr, "\n");
-	fprintf(stderr, "About:   Check sample identity. With no -g VCF given, multi-sample cross-check is performed.\n");
-	fprintf(stderr, "Usage:   bcftools gtcheck [options] [-g <genotypes.bcf>|<genotypes.vcf.gz>] <query.bcf>|<query.vcf.gz>\n");
+	fprintf(stderr, "About:   Check sample identity. With no -g BCF given, multi-sample cross-check is performed.\n");
+	fprintf(stderr, "Usage:   bcftools gtcheck [options] [-g <genotypes.vcf.gz>] <query.vcf.gz>\n");
     fprintf(stderr, "\n");
 	fprintf(stderr, "Options:\n");
 	fprintf(stderr, "    -a, --all-sites                 output comparison for all sites\n");

vcfisec.c

@@ -301,7 +301,7 @@ static void usage(void)
 {
     fprintf(stderr, "\n");
 	fprintf(stderr, "About:   Create intersections, unions and complements of VCF files.\n");
-	fprintf(stderr, "Usage:   bcftools isec [options] <A.bcf>|<A.vcf.gz> <B.bcf>|<B.vcf.gz> [...]\n");
+	fprintf(stderr, "Usage:   bcftools isec [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
     fprintf(stderr, "\n");
 	fprintf(stderr, "Options:\n");
 	fprintf(stderr, "    -c, --collapse <string>           treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");

vcfmerge.c

@@ -1688,7 +1688,7 @@ static void usage(void)
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Merge multiple VCF or BCF files to create one multi-sample file combining compatible records\n");
     fprintf(stderr, "         into one according to the -m option.\n");
-    fprintf(stderr, "Usage:   bcftools merge [options] <A.bcf>|<A.vcf.gz> <B.bcf>|<B.vcf.gz> [...]\n");
+    fprintf(stderr, "Usage:   bcftools merge [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "        --use-header <file>            use the provided header\n");

vcfnorm.c

@@ -508,7 +508,7 @@ static void usage(void)
 {
     fprintf(stderr, "\n");
 	fprintf(stderr, "About:   Left-align and normalize indels.\n");
-	fprintf(stderr, "Usage:   bcftools norm [options] -f <ref.fa> <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n");
+	fprintf(stderr, "Usage:   bcftools norm [options] -f <ref.fa> <in.vcf.gz>\n");
     fprintf(stderr, "\n");
 	fprintf(stderr, "Options:\n");
 	fprintf(stderr, "    -D, --remove-duplicates           remove duplicate lines of the same type. [Todo: merge genotypes, don't just throw away.]\n");

vcfquery.c

@@ -643,7 +643,7 @@ static void usage(void)
 {
     fprintf(stderr, "\n");
 	fprintf(stderr, "About:   Extracts fields from VCF/BCF file and prints them in user-defined format\n");
-	fprintf(stderr, "Usage:   bcftools query [options] <A.bcf>|<A.vcf>|<A.vcf.gz>|- [<B.bcf>|<B.vcf.gz> ...]\n");
+	fprintf(stderr, "Usage:   bcftools query [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
     fprintf(stderr, "\n");
 	fprintf(stderr, "Options:\n");
 	fprintf(stderr, "    -a, --annots <list>               alias for -f '%%CHROM\\t%%POS\\t%%MASK\\t%%REF\\t%%ALT\\t%%TYPE\\t' + tab-separated <list> of tags\n");

vcfroh.c

@@ -721,7 +721,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   HMM model for detecting runs of autozygosity.\n");
-    fprintf(stderr, "Usage:   bcftools roh [options] <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n");
+    fprintf(stderr, "Usage:   bcftools roh [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "General Options:\n");
     fprintf(stderr, "    -b, --biallelic-sites              consider only bi-allelic sites\n");

vcfview.c

@@ -339,7 +339,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   VCF/BCF conversion, view, subset and filter VCF/BCF files.\n");
-    fprintf(stderr, "Usage:   bcftools view [options] <in.bcf>|<in.vcf>|<in.vcf.gz>|- [region1 [...]]\n");
+    fprintf(stderr, "Usage:   bcftools view [options] <in.vcf.gz> [region1 [...]]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Output options:\n");
     fprintf(stderr, "    -G,   --drop-genotypes              drop individual genotype information (after subsetting if -s option set)\n");