Description: correct the samtools includes to match standard paths
Author: Michael R. Crusoe <crusoe@ucdavis.edu>
--- rsem.orig/BamConverter.h
+++ rsem/BamConverter.h
@@ -8,8 +8,8 @@
 #include<map>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 #include "sam_rsem_aux.h"
 #include "sam_rsem_cvt.h"
 
--- rsem.orig/BamWriter.h
+++ rsem/BamWriter.h
@@ -10,8 +10,8 @@
 #include<iostream>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 #include "sam_rsem_aux.h"
 #include "sam_rsem_cvt.h"
 
--- rsem.orig/SamParser.h
+++ rsem/SamParser.h
@@ -8,8 +8,8 @@
 #include<cassert>
 #include<string>
 
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 
 #include "utils.h"
 #include "my_assert.h"
--- rsem.orig/bc_aux.h
+++ rsem/bc_aux.h
@@ -4,7 +4,7 @@
 #include<map>
 
 #include <stdint.h>
-#include "sam/bam.h"
+#include "samtools/bam.h"
 
 struct SingleEndT {
 	bam1_t *b;
--- rsem.orig/sam_rsem_aux.h
+++ rsem/sam_rsem_aux.h
@@ -5,7 +5,7 @@
 #include<cstring>
 #include<stdint.h>
 
-#include "sam/bam.h"
+#include "samtools/bam.h"
 
 // dwt: duplicate without text
 bam_header_t *bam_header_dwt(const bam_header_t *ori_h)
--- rsem.orig/sam_rsem_cvt.h
+++ rsem/sam_rsem_cvt.h
@@ -4,7 +4,7 @@
 #include<vector>
 
 #include "stdint.h"
-#include "sam/bam.h"
+#include "samtools/bam.h"
 
 #include "Transcript.h"
 #include "Transcripts.h"
--- rsem.orig/getUnique.cpp
+++ rsem/getUnique.cpp
@@ -6,8 +6,8 @@
 #include<vector>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 
 #include "utils.h"
 
--- rsem.orig/samValidator.cpp
+++ rsem/samValidator.cpp
@@ -6,8 +6,8 @@
 #include<set>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 
 #include "utils.h"
 #include "my_assert.h"
--- rsem.orig/scanForPairedEndReads.cpp
+++ rsem/scanForPairedEndReads.cpp
@@ -7,8 +7,8 @@
 #include<algorithm>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 
 #include "utils.h"
 #include "my_assert.h"
--- rsem.orig/wiggle.cpp
+++ rsem/wiggle.cpp
@@ -4,8 +4,8 @@
 #include <iostream>
 
 #include <stdint.h>
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include "samtools/bam.h"
+#include "samtools/sam.h"
 
 #include "utils.h"
 #include "wiggle.h"
