updated alternative header reading mechanism to only work for VCF files

hts_utils.cpp

@@ -441,6 +441,7 @@ void bcf_print_lite_sorted(bcf_hdr_t *h, bcf1_t *v)
  * allow for an alternative header file to be read in.
  *
  * this searches for the alternative header saved as <filename>.hdr
+ * If the VCF files is BCF, any alternative header is ignored.
  */
 bcf_hdr_t *bcf_alt_hdr_read(htsFile *fp)
 {
@@ -451,7 +452,8 @@ bcf_hdr_t *bcf_alt_hdr_read(htsFile *fp)
     kputs(fp->fn, &alt_hdr_fn);
     kputs(".hdr", &alt_hdr_fn);
     FILE *file = fopen(alt_hdr_fn.s, "r");
-    if (!file)
+
+    if (fp->format.format ==bcf || !file)
     {
         h = bcf_hdr_read(fp);
     }

hts_utils.h

@@ -254,6 +254,7 @@ int32_t bcf_hdr_get_n_sample(bcf_hdr_t *h);
  * allow for an alternative header file to be read in.
  *
  * this searches for the alternative header saved as <filename>.hdr
+ * If the VCF files is BCF, any alternative header is ignored.
  */
 bcf_hdr_t *bcf_alt_hdr_read(htsFile *fp);
 

main.cpp

@@ -102,6 +102,7 @@ void help()
     std::clog << "view                      view vcf/vcf.gz/bcf files\n";
     std::clog << "index                     index vcf.gz/bcf files\n";
     std::clog << "normalize                 normalize variants\n";
+    std::clog << "decompose                 decompose variants\n";
     std::clog << "uniq                      drop duplicate variants\n";
     std::clog << "cat                       concatenate VCF files\n";
     std::clog << "paste                     paste VCF files\n";
@@ -110,7 +111,10 @@ void help()
     std::clog << "\n";
     std::clog << "peek                      summary of variants in the vcf file\n";
     std::clog << "partition                 partition variants\n";
+    std::clog << "multi_partition           partition variants from multiple VCF files\n";
     std::clog << "annotate_variants         annotate variants\n";
+    std::clog << "annotate_db_rsid          annotate variants with dbSNP rsid\n";
+    std::clog << "annotate_1000g            annotate variants with 1000 Genomes variants\n";
     std::clog << "annotate_regions          annotate regions\n";
     std::clog << "compute_concordance       compute genotype concordance between 2 call sets\n";
     std::clog << "compute_features          compute genotype likelihood based statistics\n";

paste.cpp

@@ -66,11 +66,12 @@ class Igor : Program
         try
         {
             std::string desc = "Pastes VCF files like the unix paste functions.\n"
+                 "              This is used after the per sample genotyping step in vt.\n"
                  "              Input requirements and assumptions:\n"
                  "              1. Same variants are represented in the same order for each file (required)\n"
                  "              2. Genotype fields are the same for corresponding records (required)\n"
                  "              3. Sample names are different in all the files (warning will be given if not)\n"
-                 "              4. Headers are the same for all the files (assumption, not checked, will fail if output is BCF)\n"
+                 "              4. Headers (not including the samples) are the same for all the files (unchecked assumption, will fail if output is BCF)\n"
                  "              Outputs:\n"
                  "              1. INFO fields output will be that of the first file\n"
                  "              2. Genotype fields are the same for corresponding records\n";