Fixed compatability issues with htslib-1.10+

Makefile.am

@@ -8,7 +8,7 @@ AM_CPPFLAGS = -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -
 noinst_HEADERS = \
 	Constant.h pException.h \
 	genomeLoci.h \
-	bcf_variant_key.h bcf_filter_arg.h
+	bcf_variant_key.h bcf_filter_arg.h bcftools.h
 
 bin_PROGRAMS = demuxlet
 

bcftools.h

@@ -0,0 +1,108 @@
+/*  bcftools.h -- utility function declarations.
+
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Petr Danecek <[email protected]>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef BCFTOOLS_H
+#define BCFTOOLS_H
+
+#include <stdarg.h>
+#include <math.h>
+
+extern "C" {
+#include "htslib/hts_defs.h"
+#include "htslib/vcf.h"
+}
+
+
+#define FT_TAB_TEXT 0       // custom tab-delimited text file
+#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)
+
+char *bcftools_version(void);
+
+/// Report an error and exit -1
+void error(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);
+
+/// Report an error and exit -1.  If errno != 0, appends strerror(errno).
+//  Note: unlike error() above, the message should not end with "\n" as a
+//  newline will be added by the function.
+void error_errno(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);
+
+void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd);
+const char *hts_bcf_wmode(int file_type);
+
+void *smalloc(size_t size);     // safe malloc
+
+static inline char gt2iupac(char a, char b)
+{
+    static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} };
+    if ( a>='a' ) a -= 'a' - 'A';
+    if ( b>='a' ) b -= 'a' - 'A';
+    if ( a=='A' ) a = 0;
+    else if ( a=='C' ) a = 1;
+    else if ( a=='G' ) a = 2;
+    else if ( a=='T' ) a = 3;
+    else return 'N';
+    if ( b=='A' ) b = 0;
+    else if ( b=='C' ) b = 1;
+    else if ( b=='G' ) b = 2;
+    else if ( b=='T' ) b = 3;
+    else return 'N';
+    return iupac[(int)a][(int)b];
+}
+
+static inline int iupac_consistent(char iupac, char nt)
+{
+    static const char iupac_mask[90] = {
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,14,2,
+        13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10
+    };
+    if ( iupac > 89 ) return 0;
+    if ( nt > 90 ) nt -=  32;  // lowercase 
+    if ( nt=='A' ) nt = 1;
+    else if ( nt=='C' ) nt = 2;
+    else if ( nt=='G' ) nt = 4;
+    else if ( nt=='T' ) nt = 8;
+    return iupac_mask[(int)iupac] & nt ? 1 : 0;
+}
+
+static inline char nt_to_upper(char nt)
+{
+    if ( nt < 97 ) return nt;
+    return nt - 32;
+}
+
+static inline double phred_score(double prob)
+{
+    if ( prob==0 ) return 99;
+    prob = -4.3429*log(prob);
+    return prob>99 ? 99 : prob;
+}
+
+#endif