Release 1.3.2: bin field bug fix, RTLD_GLOBAL plugins

Makefile

@@ -92,7 +92,7 @@ HTSPREFIX =
 include htslib_vars.mk
 
 
-PACKAGE_VERSION  = 1.3.1
+PACKAGE_VERSION  = 1.3.2
 LIBHTS_SOVERSION = 1
 
 

NEWS

@@ -1,4 +1,15 @@
-Noteworthy changes in release 1.3.1 (22 April 2016)
+Noteworthy changes in release 1.3.2  (13 September 2016)
+
+* Corrected bin calculation when converting directly from CRAM to BAM.
+  Previously a small fraction of converted reads would fail Picard's
+  validation with "bin field of BAM record does not equal value computed"
+  (SAMtools issue #574).
+
+* Plugins can now signal to HTSlib which of RTLD_LOCAL and RTLD_GLOBAL
+  they wish to be opened with -- previously they were always RTLD_LOCAL.
+
+
+Noteworthy changes in release 1.3.1  (22 April 2016)
 
 * Improved error checking and reporting, especially of I/O errors when
   writing output files (#17, #315, PR #271, PR #317).

cram/cram_io.c

@@ -86,6 +86,10 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "htslib/bgzf.h"
 #include "htslib/faidx.h"
 
+#ifndef PATH_MAX
+#define PATH_MAX FILENAME_MAX
+#endif
+
 #define TRIAL_SPAN 50
 #define NTRIALS 3
 

cram/cram_samtools.c

@@ -90,7 +90,7 @@ int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
 
     b->core.tid     = rname;
     b->core.pos     = pos-1;
-    b->core.bin     = bam_reg2bin(pos, end);
+    b->core.bin     = bam_reg2bin(pos-1, end);
     b->core.qual    = mapq;
     b->core.l_qname = qname_len+1;
     b->core.flag    = flag;

hfile.c

@@ -577,8 +577,6 @@ static hFILE *hopen_mem(const char *data, const char *mode)
  * Plugin and hopen() backend dispatcher *
  *****************************************/
 
-#include <ctype.h>
-
 #include "hts_internal.h"
 #include "htslib/khash.h"
 
@@ -717,8 +715,8 @@ static const struct hFILE_scheme_handler *find_scheme_handler(const char *s)
     int i;
 
     for (i = 0; i < sizeof scheme; i++)
-        if (isalnum(s[i]) || s[i] == '+' || s[i] == '-' || s[i] == '.')
-            scheme[i] = tolower(s[i]);
+        if (isalnum_c(s[i]) || s[i] == '+' || s[i] == '-' || s[i] == '.')
+            scheme[i] = tolower_c(s[i]);
         else if (s[i] == ':') break;
         else return NULL;
 

hts.c

@@ -26,7 +26,6 @@ DEALINGS IN THE SOFTWARE.  */
 #include <config.h>
 
 #include <zlib.h>
-#include <ctype.h>
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
@@ -1848,24 +1847,24 @@ long long hts_parse_decimal(const char *str, char **strend, int flags)
     char sign = '+', esign = '+';
     const char *s;
 
-    while (isspace(*str)) str++;
+    while (isspace_c(*str)) str++;
     s = str;
 
     if (*s == '+' || *s == '-') sign = *s++;
     while (*s)
-        if (isdigit(*s)) n = push_digit(n, *s++);
+        if (isdigit_c(*s)) n = push_digit(n, *s++);
         else if (*s == ',' && (flags & HTS_PARSE_THOUSANDS_SEP)) s++;
         else break;
 
     if (*s == '.') {
         s++;
-        while (isdigit(*s)) decimals++, n = push_digit(n, *s++);
+        while (isdigit_c(*s)) decimals++, n = push_digit(n, *s++);
     }
 
     if (*s == 'E' || *s == 'e') {
         s++;
         if (*s == '+' || *s == '-') esign = *s++;
-        while (isdigit(*s)) e = push_digit(e, *s++);
+        while (isdigit_c(*s)) e = push_digit(e, *s++);
         if (esign == '-') e = -e;
     }
 

htsfile.1

@@ -1,4 +1,4 @@
-.TH htsfile 1 "22 April 2016" "htslib-1.3.1" "Bioinformatics tools"
+.TH htsfile 1 "13 September 2016" "htslib-1.3.2" "Bioinformatics tools"
 .SH NAME
 htsfile \- identify high-throughput sequencing data files
 .\"

plugin.c

@@ -135,13 +135,35 @@ const char *hts_path_itr_next(struct hts_path_itr *itr)
     return NULL;
 }
 
+
+#ifndef RTLD_NOLOAD
+#define RTLD_NOLOAD 0
+#endif
+
 void *load_plugin(void **pluginp, const char *filename, const char *symbol)
 {
     void *lib = dlopen(filename, RTLD_NOW | RTLD_LOCAL);
     if (lib == NULL) goto error;
 
     void *sym = dlsym(lib, symbol);
-    if (sym == NULL) goto error;
+    if (sym == NULL) {
+        // Reopen the plugin with RTLD_GLOBAL and check for uniquified symbol
+        void *libg = dlopen(filename, RTLD_NOLOAD | RTLD_NOW | RTLD_GLOBAL);
+        if (libg == NULL) goto error;
+        dlclose(lib);
+        lib = libg;
+
+        kstring_t symbolg = { 0, 0, NULL };
+        kputs(symbol, &symbolg);
+        kputc('_', &symbolg);
+        const char *slash = strrchr(filename, '/');
+        const char *basename = slash? slash+1 : filename;
+        kputsn(basename, strcspn(basename, ".-+"), &symbolg);
+
+        sym = dlsym(lib, symbolg.s);
+        free(symbolg.s);
+        if (sym == NULL) goto error;
+    }
 
     *pluginp = lib;
     return sym;

sam.c

@@ -29,7 +29,6 @@ DEALINGS IN THE SOFTWARE.  */
 #include <stdlib.h>
 #include <string.h>
 #include <errno.h>
-#include <ctype.h>
 #include <zlib.h>
 #include "htslib/sam.h"
 #include "htslib/bgzf.h"
@@ -888,7 +887,7 @@ int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
         uint32_t *cigar;
         size_t n_cigar = 0;
         for (q = p; *p && *p != '\t'; ++p)
-            if (!isdigit(*p)) ++n_cigar;
+            if (!isdigit_c(*p)) ++n_cigar;
         if (*p++ != '\t') goto err_ret;
         _parse_err(n_cigar == 0, "no CIGAR operations");
         _parse_err(n_cigar >= 65536, "too many CIGAR operations");

tabix.1

@@ -1,4 +1,4 @@
-.TH tabix 1 "22 April 2016" "htslib-1.3.1" "Bioinformatics tools"
+.TH tabix 1 "13 September 2016" "htslib-1.3.2" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip \- Block compression/decompression utility