@@ -7,11 +7,11 @@ Description: This package implements a model of per-position sequencing

         bias in high-throughput sequencing data using a simple Bayesian

         network, the structure and parameters of which are trained on a

         set of aligned reads and a reference genome sequence.

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

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

+Author: Daniel Jones <djones3@fredhutch.org>

+Maintainer: Daniel Jones <djones3@fredhutch.org>

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

         2.15.0), methods

-LinkingTo: Rhtslib (>= 1.15.3)

+LinkingTo: Rhtslib (>= 1.99.1), zlibbioc

 SystemRequirements: GNU make

 Suggests: Rsamtools, ggplot2

 LazyLoad: yes

@@ -12,6 +12,9 @@ RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \

 PKG_LIBS=$(RHTSLIB_LIBS)

 PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS)

+$(info $$SEQBIAS_OBJ is [${SEQBIAS_OBJ}])

+$(info $$YAML_CPP_OBJ is [${YAML_CPP_OBJ}])

+

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

 all : $(SHLIB)

@@ -5,12 +5,7 @@ YAML_CPP_OBJ = aliasmanager.o conversion.o directives.o \

                regex.o scanner.o scanscalar.o scantag.o scantoken.o \

                simplekey.o singledocparser.o stream.o tag.o

-

-

-SEQBIAS_OBJ = sam.o \

-              bam_plbuf.o \

-              bam_aux.o \

-              common.o \

+SEQBIAS_OBJ = common.o \

               miscmath.o \

               pos_table.o \

               kmer_matrix.o \

@@ -1,6 +1,7 @@

 #include "pos_table.h"

 #include "logger.h"

+#include <samtools-1.7-compat.h>

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

 #include <stdint.h>

 #include <stdlib.h>

 #include <stdbool.h>

-#include "sam.h"

+#include <htslib/sam.h>

 /* The table maps positions to counts. */

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

 extern "C" {

-#include "htslib/faidx.h"

-#include "sam.h"

+#include <htslib/faidx.h>

+#include <samtools-1.7-compat.h>

 #ifdef ERROR

@@ -16,6 +16,7 @@

 #include <ctime>

 #include <fstream>

 #include <algorithm>

+#include <samtools-1.7-compat.h>

 using namespace std;