@@ -1,6 +1,6 @@

 Package: seqbias

-Version: 1.31.0

-Date: 25-12-2010

+Version: 1.31.1

+Date: 2019-03-15

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

         data

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

@@ -9,10 +9,9 @@ Description: This package implements a model of per-position sequencing

         set of aligned reads and a reference genome sequence.

 Author: Daniel Jones <dcjones@cs.washington.edu>

 Maintainer: Daniel Jones <dcjones@cs.washington.edu>

-Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=

+Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=

         2.15.0), methods

-LinkingTo: Rsamtools (>= 1.19.38)

-Imports: zlibbioc

+LinkingTo: Rhtslib (>= 1.15.3)

 Suggests: Rsamtools, ggplot2

 LazyLoad: yes

 License: LGPL-3

@@ -1,3 +1,2 @@

 exportPattern("^[^\\.]")

 useDynLib(seqbias)

-import(zlibbioc)

@@ -1,19 +1,14 @@

 include Makevars.common

-SAMTOOLS_PATH=\

-    `echo 'cat(system.file("usrlib", .Platform[["r_arch"]], \

-        package="Rsamtools", mustWork=TRUE))' |\

-        "${R_HOME}/bin/R" --vanilla --slave`

-SAMTOOLS_LIBS="$(SAMTOOLS_PATH)/libbam.a" "$(SAMTOOLS_PATH)/libbcf.a"\

-    "$(SAMTOOLS_PATH)/libtabix.a" -lz -pthread

-SAMTOOLS_CPPFLAGS=-D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 \

-    -D_LARGEFILE64_SOURCE

+RHTSLIB_LIBS=`echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\

+    "${R_HOME}/bin/R" --vanilla --slave`

+RHTSLIB_CPPFLAGS=`echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\

+    "${R_HOME}/bin/R" --vanilla --slave`

-PKG_LIBS=$(SAMTOOLS_LIBS)

-PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS)

+PKG_LIBS=$(RHTSLIB_LIBS)

+PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)

-OBJECTS = $(SEQBIAS_OBJ) \

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

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

 all : $(SHLIB)

@@ -7,10 +7,12 @@ YAML_CPP_OBJ = aliasmanager.o conversion.o directives.o \

-SEQBIAS_OBJ = common.o \

+SEQBIAS_OBJ = sam.o \

+              bam_plbuf.o \

+              bam_aux.o \

+              common.o \

               miscmath.o \

               pos_table.o \

-              samtools_extra.o \

               kmer_matrix.o \

               logger.o \

               motif.o \

@@ -1,15 +1,14 @@

 include Makevars.common

-SAMVARS=$(shell echo 'cat(system.file("usretc", .Platform[["r_arch"]],\

-    "Rsamtools.mk", package="Rsamtools", mustWork=TRUE))' |\

+RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\

+    "${R_HOME}/bin/R" --vanilla --slave)

+RHTSLIB_CPPFLAGS=$(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\

     "${R_HOME}/bin/R" --vanilla --slave)

-include $(SAMVARS)

-PKG_LIBS=$(SAMTOOLS_LIBS)

-PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS)

+PKG_LIBS=$(RHTSLIB_LIBS)

+PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)

-OBJECTS = $(SEQBIAS_OBJ) \

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

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

 all : $(SHLIB)

new file mode 100644

@@ -0,0 +1 @@

+#include <bam_aux.c>

new file mode 100644

@@ -0,0 +1 @@

+#include <bam_plbuf.c>

@@ -24,7 +24,7 @@ extern "C" {

 #include <stdint.h>

 #include <stdlib.h>

 #include <stdbool.h>

-#include "samtools/sam.h"

+#include "sam.h"

 /* The table maps positions to counts. */

new file mode 100644

@@ -0,0 +1 @@

+#include <sam.c>

deleted file mode 100644

@@ -1,100 +0,0 @@

-

-#include "logger.h"

-#include "samtools_extra.h"

-#include "samtools/khash.h"

-

-

-#ifndef _NO_RAZF

-#include "samtools/razf.h"

-#else

-#ifdef _WIN32

-#define ftello(fp) ftell(fp)

-#define fseeko(fp, offset, whence) fseek(fp, offset, whence)

-#else

-extern off_t ftello(FILE *stream);

-extern int fseeko(FILE *stream, off_t offset, int whence);

-#endif

-#define RAZF FILE

-#define razf_read(fp, buf, size) fread(buf, 1, size, fp)

-#define razf_open(fn, mode) fopen(fn, mode)

-#define razf_close(fp) fclose(fp)

-#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)

-#define razf_tell(fp) ftello(fp)

-#endif

-#ifdef _USE_KNETFILE

-#include "samtools/knetfile.h"

-#endif

-

-#include <ctype.h>

-

-

-typedef struct {

-	int32_t line_len, line_blen;

-	int64_t len;

-	uint64_t offset;

-} faidx1_t;

-KHASH_MAP_INIT_STR(s, faidx1_t)

-

-

-struct __faidx_t {

-	RAZF *rz;

-	int n, m;

-	char **name;

-	khash_t(s) *hash;

-};

-

-

-

-

-char* faidx_fetch_seq_forced_lower( const faidx_t* fai, const char *c_name, int p_beg_i, int p_end_i )

-{

-

-	int l;

-	char c;

-    khiter_t iter;

-    faidx1_t val;

-    char* seq0;

-    char* seq = NULL;

-

-    iter = kh_get(s, fai->hash, c_name);

-    if(iter == kh_end(fai->hash)) return 0;

-

-    seq0 = seq = (char*)malloc( (p_end_i - p_beg_i + 2) * sizeof(char) );

-    if( seq0 == NULL ) logger_abort("Out of memory.");

-    seq0[p_end_i-p_beg_i+1] = '\0';

-

-    val = kh_value(fai->hash, iter);

-

-    /* entirely off the map: all Ns */

-    if( p_beg_i >= (int)val.len || p_end_i < 0 ) {

-        while( p_beg_i <= p_end_i ) {

-            *seq++ ='n';

-            ++p_beg_i;

-        }

-        return seq0;

-    }

-

-    /* beginning is off the map */

-    while( p_beg_i < 0 && p_beg_i <= p_end_i ) {

-        *seq++ = 'n';

-        p_beg_i++;

-    }

-

-    /* end is off the map */

-    while( p_end_i >= (int)val.len ) {

-        seq[p_end_i-p_beg_i] = 'n';

-        p_end_i--;

-    }

-

-    /* retrieve the sequence */

-	l = 0;

-	razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);

-	while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)

-		if (isgraph(c)) seq[l++] = tolower(c);

-    

-    while( p_beg_i+l <= p_end_i ) seq[l++] = 'n';

-

-    return seq0;

-}

-

-

deleted file mode 100644

@@ -1,32 +0,0 @@

-

-#ifndef ISOLATOR_SAMTOOLS_EXTRA_H

-#define ISOLATOR_SAMTOOLS_EXTRA_H

-

-#ifdef __cplusplus

-extern "C" {

-#endif

-

-

-#include "samtools/faidx.h"

-#include "samtools/bam.h"

-

-

-/* exposing a function defined in samtools/bam_aux.c */

-void bam_init_header_hash(bam_header_t *header);

-

-

-/* Change the behavior of the faidx_fetch_seq function to be more useful. If

- * coordinates are outside the actual sequence, write N's, rather than adjusting

- * the start,end. */

-char* faidx_fetch_seq_forced_lower(const faidx_t* fai, const char *c_name, int p_beg_i, int p_end_i);

-

-

-

-#ifdef __cplusplus

-}

-#endif

-

-

-#endif

-

-

@@ -10,8 +10,8 @@

 extern "C" {

-#include "samtools/faidx.h"

-#include "samtools/sam.h"

+#include "htslib/faidx.h"

+#include "sam.h"

 #ifdef ERROR

@@ -9,8 +9,7 @@

 #include "logger.hpp"

 #include "twobitseq.hpp"

 #include "miscmath.h"

-#include "samtools_extra.h"

-#include "samtools/faidx.h"

+#include "htslib/faidx.h"

 #include <climits>

 #include <cmath>

 #include <cctype>

@@ -219,7 +218,7 @@ void sequencing_bias::build(const char* ref_fn,

         logger::abort("Can't open bam index '%s.bai'.", reads_fn);

     }

-    bam_init_header_hash(reads_f->header);

+    //bam_init_header_hash(reads_f->header);

     bam1_t* read = bam_init1();

@@ -485,7 +484,7 @@ kmer_matrix tabulate_bias(double* kl,

     }

-    bam_init_header_hash(reads_f->header);

+    //bam_init_header_hash(reads_f->header);

     bam1_t* read = bam_init1();

     pos_table T;

@@ -12,7 +12,7 @@

 #include "common.h"

 #include "motif.hpp"

 #include "pos_table.h"

-#include "samtools/faidx.h"

+#include "htslib/faidx.h"

 #include "yaml-cpp/yaml.h"

 #include <string>