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

 Package: seqbias

-Version: 0.99.8

+Version: 0.99.9

 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

@@ -16,5 +16,5 @@ 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

+PKG_CFLAGS  += -Wall -D_GNU_SOURCE

@@ -11,8 +11,15 @@ extern "C" {

 #ifndef NEED_ASPRINTF

 #include <stdio.h>

 #else

-int asprintf (char **resultp, const char *format, ...);

+

+#include <stdarg.h>

+

 /* defined in gnulib/asprintf.c */

+int asprintf (char **resultp, const char *format, ...);

+

+/* defined in gnulib/vasprintf.c */

+int vasprintf(char **strp, const char *fmt, va_list ap);

+

 #endif

@@ -368,12 +368,12 @@ void sequencing_bias::build( const char* ref_fn,

         /* add a foreground sequence */

         if( S[i].strand ) {

-            if( S[i].pos < R ) continue;

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

             memcpy( local_seq, seq + S[i].pos - R, (L+1+R)*sizeof(char) );

             seqrc( local_seq, L+1+R );

         }

         else {

-            if( S[i].pos < L ) continue;

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

             memcpy( local_seq, seq + (S[i].pos-L), (L+1+R)*sizeof(char) );

         }

@@ -388,12 +388,12 @@ void sequencing_bias::build( const char* ref_fn,

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

             if( S[i].strand ) {

-                if( bg_pos < R ) continue;

+                if( bg_pos < R || S[i].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 ) continue;

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

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

             }