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

 Package: seqbias

-Version: 0.99.10

+Version: 0.99.11

 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

@@ -1,5 +1,13 @@

 include Makevars.common

+PKG_CFLAGS   += -D_GNU_SOURCE

+PKG_CXXFLAGS += -D_GNU_SOURCE

+

 OBJECTS = $(SEQBIAS_OBJ) \

 		  $(YAML_CPP_OBJ:%=yaml-cpp/%)

+all : $(SHLIB)

+

+clean :

+	rm -rf $(OBJECTS)

+

@@ -16,5 +16,6 @@ SEQBIAS_OBJ = sequencing_bias.o kmers.o miscmath.o common.o \

 GNULIB_OBJ = asprintf.o printf-args.o printf-parse.o vasnprintf.o vasprintf.o

-PKG_CFLAGS  += -Wall -D_GNU_SOURCE

+PKG_CFLAGS   += -Wall

+PKG_CXXFLAGS += -Wall

@@ -1,5 +1,13 @@

 include Makevars.common

+

 PKG_CPPFLAGS+=-DNEED_ASPRINTF

+

 OBJECTS = $(SEQBIAS_OBJ) \

 		  $(YAML_CPP_OBJ:%=yaml-cpp/%) \

 		  $(GNULIB_OBJ:%=gnulib/%)

+

+all : $(SHLIB)

+

+clean :

+	rm -rf $(OBJECTS)

+

@@ -70,11 +70,11 @@ 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;

@@ -335,13 +335,13 @@ 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;

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

     out << YAML::Key << "parents";

     out << YAML::Value;

@@ -722,7 +722,7 @@ void train_motifs( motif& M0, motif& M1,

     while( true ) {

         round_num++;

-        log_printf( LOG_MSG, "round %4d (ic = %0.4e) ", round_num, ic_curr );

+        log_printf( LOG_MSG, "round %4zu (ic = %0.4e) ", round_num, ic_curr );

         col = 0;

         ic_forw_best = ic_back_best = ic_rev_best = -HUGE_VAL;

@@ -383,21 +383,22 @@ void sequencing_bias::build( const char* ref_fn,

         /* add a background sequence */

         /* adjust the current read position randomly, and sample */

-        for( bg_sample_num = 0; bg_sample_num < bg_samples; bg_sample_num++ ) {

+        for( bg_sample_num = 0; bg_sample_num < bg_samples; ) {

             bg_pos = S[i].pos + (pos)ceil( rand_trunc_gauss( offset_std, -100, 100 ) );

             if( S[i].strand ) {

-                if( bg_pos < R || S[i].pos >= seqlen - L ) continue;

+                if( bg_pos < R || bg_pos >= seqlen - L ) continue;

                 memcpy( local_seq, seq + bg_pos - R, (L+1+R)*sizeof(char) );

                 seqrc( local_seq, L+1+R );

             }

             else {

-                if( bg_pos < L || S[i].pos >= seqlen - R ) continue;

+                if( bg_pos < L || bg_pos >= seqlen - R ) continue;

                 memcpy( local_seq, seq + (bg_pos-L), (L+1+R)*sizeof(char) );

             }

             training_seqs.push_back( new sequence( local_seq, 0 ) );

+            bg_sample_num++;

         }

     }