@@ -1,5 +1,5 @@

 Package: seqbias

-Version: 0.99.2

+Version: 0.99.3

 Date: 25-12-2010

 Title: Estimation of per-position bias in high-throughput sequencing data

 Description: This package implements a model of per-position sequencing bias in

@@ -119,6 +119,7 @@ configure:2948: checking for pow

 configure:2948: gcc -o conftest -g -O2   conftest.c -lz  >&5

 conftest.c:35: warning: conflicting types for built-in function 'pow'

 /tmp/cc2oJinr.o: In function `main':

+/tmp/ccFHWg6Y.o: In function `main':

 /home/dcjones/bio/seqbias/conftest.c:46: undefined reference to `pow'

 collect2: ld returned 1 exit status

 configure:2948: $? = 1

@@ -176,7 +177,11 @@ configure:2948: result: no

 configure:2948: checking for sqrt

 configure:2948: gcc -o conftest -g -O2   conftest.c -lz  >&5

 conftest.c:35: warning: conflicting types for built-in function 'sqrt'

+<<<<<<< HEAD

 /tmp/ccFdFAsw.o: In function `main':

+=======

+/tmp/ccgUY6M3.o: In function `main':

+>>>>>>> working

 /home/dcjones/bio/seqbias/conftest.c:46: undefined reference to `sqrt'

 collect2: ld returned 1 exit status

 configure:2948: $? = 1

@@ -1,22 +1,8 @@

-SAMTOOLS_OBJ = bam_aux.o bam.o bam_import.o bam_index.o bam_pileup.o \

-               bgzf.o faidx.o knetfile.o kstring.o razf.o sam.o sam_header.o

-              

-YAML_CPP_OBJ = aliascontent.o conversion.o emitter.o emitterstate.o \

-               emitterutils.o exp.o iterator.o map.o node.o null.o \

-               ostream.o parser.o parserstate.o regex.o scalar.o scanner.o \

-               scanscalar.o scantag.o scantoken.o sequence.o simplekey.o \

-               stream.o tag.o

-

-SEQBIAS_OBJ = sequencing_bias.o kmers.o miscmath.o common.o \

-			  table.o superfasthash.o logger.o seqbias.o \

-			  snprintf.o

+PKG_LIBS+=-lz 

-DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64

-PKG_CFLAGS  += $(DFLAGS)

-PKG_CPPFLAGS = $(PKG_CFLAGS)

+include Makevars.common

-PKG_LIBS+=-lz 

 OBJECTS = $(SEQBIAS_OBJ) $(SAMTOOLS_OBJ:%=samtools/%) $(YAML_CPP_OBJ:%=yaml-cpp/%)

new file mode 100644

@@ -0,0 +1,18 @@

+

+SAMTOOLS_OBJ = bam_aux.o bam.o bam_import.o bam_index.o bam_pileup.o \

+               bgzf.o faidx.o knetfile.o kstring.o razf.o sam.o sam_header.o

+              

+YAML_CPP_OBJ = aliascontent.o conversion.o emitter.o emitterstate.o \

+               emitterutils.o exp.o iterator.o map.o node.o null.o \

+               ostream.o parser.o parserstate.o regex.o scalar.o scanner.o \

+               scanscalar.o scantag.o scantoken.o sequence.o simplekey.o \

+               stream.o tag.o

+

+SEQBIAS_OBJ = sequencing_bias.o kmers.o miscmath.o common.o \

+			  table.o superfasthash.o logger.o seqbias.o \

+			  snprintf.o

+

+DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64

+PKG_CFLAGS  += $(DFLAGS) -Wall

+PKG_CPPFLAGS = $(PKG_CFLAGS)

+

@@ -1,22 +1,8 @@

-SAMTOOLS_OBJ = bam_aux.o bam.o bam_import.o bam_index.o bam_pileup.o \

-               bgzf.o faidx.o knetfile.o kstring.o razf.o sam.o sam_header.o

-              

-YAML_CPP_OBJ = aliascontent.o conversion.o emitter.o emitterstate.o \

-               emitterutils.o exp.o iterator.o map.o node.o null.o \

-               ostream.o parser.o parserstate.o regex.o scalar.o scanner.o \

-               scanscalar.o scantag.o scantoken.o sequence.o simplekey.o \

-               stream.o tag.o

-

-SEQBIAS_OBJ = sequencing_bias.o kmers.o miscmath.o common.o \

-			  table.o superfasthash.o logger.o seqbias.o \

-			  snprintf.o

+PKG_LIBS+=@LIBS@

-DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64

-PKG_CFLAGS  += $(DFLAGS)

-PKG_CPPFLAGS = $(PKG_CFLAGS)

+include Makevars.common

-PKG_LIBS+=@LIBS@

 OBJECTS = $(SEQBIAS_OBJ) $(SAMTOOLS_OBJ:%=samtools/%) $(YAML_CPP_OBJ:%=yaml-cpp/%)

new file mode 100644

@@ -0,0 +1,13 @@

+

+PKG_LIBS+=-$(ZLIB_LIBS) -lws2_32

+PKG_CFLAGS+=-D_LARGEFILE64_SOURCE

+

+include Makevars.common

+

+OBJECTS = $(SEQBIAS_OBJ) $(SAMTOOLS_OBJ:%=samtools/%) $(YAML_CPP_OBJ:%=yaml-cpp/%)

+

+all : $(SHLIB)

+

+clean:

+	rm -f $(OBJECTS)

+

@@ -81,11 +81,11 @@ void kmer_matrix::to_yaml( YAML::Emitter& out ) const

     out << YAML::BeginMap;

     out << YAML::Key   << "k";

-    out << YAML::Value << k;

+    out << YAML::Value << (unsigned int)k;

     out << YAML::Key   << "n";

-    out << YAML::Value << n;

+    out << YAML::Value << (unsigned int)n;

     out << YAML::Key   << "m";

-    out << YAML::Value << m;

+    out << YAML::Value << (unsigned int)m;

     out << YAML::Key   << "A";

     out << YAML::Flow;

     out << YAML::Value;

@@ -329,10 +329,10 @@ void motif::to_yaml( YAML::Emitter& out ) const

     out << YAML::BeginMap;

     out << YAML::Key   << "n";

-    out << YAML::Value << n;

+    out << YAML::Value << (unsigned int)n;

     out << YAML::Key   << "k";

-    out << YAML::Value << k;

+    out << YAML::Value << (unsigned int)k;

     out << YAML::Key   << "c";

     out << YAML::Value << c;

@@ -118,7 +118,8 @@ void failf( const char* fmt, ... )

     va_end(ap);

-    fail( outstr );

+    if( outstrlen ) fail( outstr );

+    else            fail( "" );

     free( outstr );

 }

@@ -270,7 +270,7 @@ void dealloc_kmer_matrix( SEXP M )

 SEXP seqbias_alloc_kmer_matrix( SEXP n, SEXP k )

 {

-    int c_n, c_k;

+    int c_n = 0, c_k = 0;

     if( !IS_INTEGER(n) || (c_n = asInteger(n)) <= 0) {

         error( "'n' must be a positive integer" );

@@ -306,7 +306,7 @@ SEXP seqbias_tally_kmers( SEXP M, SEXP seq, SEXP count, SEXP offset )

     pos c_offset = asInteger(offset);

     size_t n = strlen(c_seq);

-    if( LENGTH(count) != n ) error( "sequence length mismatches count length" );

+    if( (size_t)LENGTH(count) != n ) error( "sequence length mismatches count length" );

     size_t k = c_M->getk();

@@ -314,13 +314,13 @@ SEXP seqbias_tally_kmers( SEXP M, SEXP seq, SEXP count, SEXP offset )

      * Convert the sequence to an array of kmers.

      */

-    int i;

+    size_t i;

     kmer kmer_mask = 0;

     for( i = 0; i < k; i++ ) kmer_mask = (kmer_mask<<2) | 0x3;

     kmer* ks = new kmer[n - (k - 1)];

     memset( ks, 0, (n - (k - 1)) * sizeof(kmer) );

-    kmer K;

+    kmer K = 0;

     for( i = 0; i < n; i++ ) {

         K = ((K << 2) | nt2num(c_seq[i])) & kmer_mask;

         if( i >= k-1 ) ks[i-(k-1)] = K;

@@ -332,9 +332,12 @@ SEXP seqbias_tally_kmers( SEXP M, SEXP seq, SEXP count, SEXP offset )

      */

     pos j;

     for( i = 0; i < n; i++ ) {

-        if( i >= c_offset && i - c_offset + c_M->getn() <= n && REAL(count)[i] > 0.0 ) {

-            for( j = 0; j < c_M->getn(); j++ ) {

-                (*c_M)( j, ks[i - c_offset + j] ) += REAL(count)[i];

+        if( (pos)i >= c_offset &&

+            (pos)i - c_offset + c_M->getn() <= n &&

+            REAL(count)[i] > 0.0 )

+        {

+            for( j = 0; (size_t)j < c_M->getn(); j++ ) {

+                (*c_M)( j, ks[(pos)i - c_offset + j] ) += REAL(count)[i];

                 //(*c_M)( j, ks[i - c_offset + j] ) += 1;

             }

         }

@@ -371,7 +374,7 @@ SEXP seqbias_dataframe_from_kmer_matrix( SEXP M, SEXP offset )

     char* Kstr = new char[k+1];

-    for( i = 0; i < n; i++ ) {

+    for( i = 0; (size_t)i < n; i++ ) {

         for( K = 0; K < m; K++ ) {

             /* set pos */

@@ -219,10 +219,9 @@ void sequencing_bias::build( const char* ref_fn,

     /* background sampling */

     const size_t bg_samples = 1; // make this many samples for each read

-    int bg_sample_num;           // keep track of the number of samples made

+    size_t bg_sample_num;        // keep track of the number of samples made

     struct read_pos bg;          // background position being considered

-    int b;

     char*          seqname   = NULL;

     int            seqlen    = 0;

     int            curr_tid  = -1;

@@ -240,10 +240,6 @@

  * with "ap2 = ap", in this case you must not call va_end(ap2) !

  *   #define va_copy(ap2,ap) ap2 = ap

  */

-/* #define NEED_ASPRINTF   */

-/* #define NEED_ASNPRINTF  */

-/* #define NEED_VASPRINTF  */

-/* #define NEED_VASNPRINTF */

 /* Define the following macros if desired:

@@ -284,6 +280,15 @@

 /* NO USER SERVICABLE PARTS FOLLOWING THIS POINT */

 /* ============================================= */

+#ifdef _GNU_SOURCE

+#define HAVE_SNPRINTF

+#else

+#define NEED_ASPRINTF  

+#define NEED_ASNPRINTF 

+#define NEED_VASPRINTF 

+#define NEED_VASNPRINTF

+#endif

+

 #define PORTABLE_SNPRINTF_VERSION_MAJOR 2

 #define PORTABLE_SNPRINTF_VERSION_MINOR 2

@@ -157,7 +157,7 @@ int compare_seq_hash( const void* x, const void* y )

     if( c == 0 ) {

         uint32_t ha = hash( (void*)&(*a)->pos, sizeof(struct read_pos) );

         uint32_t hb = hash( (void*)&(*b)->pos, sizeof(struct read_pos) );

-        return (int32_t)a - (int32_t)b;

+        return (int32_t)ha - (int32_t)hb;

     }

     else return c;