Release 1.2.1: patch release over 1.2, reinstating hts_file_type()

Makefile

@@ -101,7 +101,7 @@ lib-shared: libhts.so
 endif
 
 
-PACKAGE_VERSION  = 1.2
+PACKAGE_VERSION  = 1.2.1
 LIBHTS_SOVERSION = 1
 
 

NEWS

@@ -1,3 +1,10 @@
+Noteworthy changes in release 1.2.1  (3 February 2015)
+
+* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
+  but briefly removed in 1.2.  This function is deprecated and will be removed
+  in a future release -- you should use hts_detect_format() etc instead
+
+
 Noteworthy changes in release 1.2  (2 February 2015)
 
 * HTSlib now has a configure script which checks your build environment

hts.c

@@ -722,6 +722,29 @@ char **hts_readlines(const char *fn, int *_n)
     return s;
 }
 
+// DEPRECATED: To be removed in a future HTSlib release
+int hts_file_type(const char *fname)
+{
+    int len = strlen(fname);
+    if ( !strcasecmp(".vcf.gz",fname+len-7) ) return FT_VCF_GZ;
+    if ( !strcasecmp(".vcf",fname+len-4) ) return FT_VCF;
+    if ( !strcasecmp(".bcf",fname+len-4) ) return FT_BCF_GZ;
+    if ( !strcmp("-",fname) ) return FT_STDIN;
+
+    hFILE *f = hopen(fname, "r");
+    if (f == NULL) return 0;
+
+    htsFormat fmt;
+    if (hts_detect_format(f, &fmt) < 0) { hclose_abruptly(f); return 0; }
+    if (hclose(f) < 0) return 0;
+
+    switch (fmt.format) {
+    case vcf: return (fmt.compression == no_compression)? FT_VCF : FT_VCF_GZ;
+    case bcf: return (fmt.compression == no_compression)? FT_BCF : FT_BCF_GZ;
+    default:  return 0;
+    }
+}
+
 /****************
  *** Indexing ***
  ****************/

htsfile.1

@@ -1,4 +1,4 @@
-.TH htsfile 1 "2 February 2015" "htslib-1.2" "Bioinformatics tools"
+.TH htsfile 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools"
 .SH NAME
 htsfile \- identify high-throughput sequencing data files
 .\"

htslib/hts.h

@@ -379,6 +379,21 @@ extern "C" {
     int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data);
     const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
 
+    /**
+     * hts_file_type() - Convenience function to determine file type
+     * DEPRECATED:  This function has been replaced by hts_detect_format().
+     * It and these FT_* macros will be removed in a future HTSlib release.
+     */
+    #define FT_UNKN   0
+    #define FT_GZ     1
+    #define FT_VCF    2
+    #define FT_VCF_GZ (FT_GZ|FT_VCF)
+    #define FT_BCF    (1<<2)
+    #define FT_BCF_GZ (FT_GZ|FT_BCF)
+    #define FT_STDIN  (1<<3)
+    int hts_file_type(const char *fname);
+
+
 #ifdef __cplusplus
 }
 #endif

tabix.1

@@ -1,4 +1,4 @@
-.TH tabix 1 "2 February 2015" "htslib-1.2" "Bioinformatics tools"
+.TH tabix 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip \- Block compression/decompression utility