Merge 785423a into fa7ea22

broadinstitute · Nov 25, 2014 · 84141b8 · 84141b8
2 parents fa7ea22 + 785423a
commit 84141b8
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Showing 48 changed files with 112 additions and 76 deletions.
diff --git a/gamgee/missing.h b/gamgee/missing.h
@@ -3,6 +3,7 @@
 
 #include "sam/sam_tag.h"
 #include "utils/utils.h"
+
 #include "htslib/vcf.h"
 
 #include <vector>

diff --git a/gamgee/sam/base_quals.cpp b/gamgee/sam/base_quals.cpp
@@ -1,6 +1,7 @@
 #include "base_quals.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
+
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
 
 #include <string>
 #include <stdexcept>

diff --git a/gamgee/sam/cigar.cpp b/gamgee/sam/cigar.cpp
@@ -1,6 +1,7 @@
 #include "cigar.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
+
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
 
 #include <string>
 #include <sstream>

diff --git a/gamgee/sam/indexed_sam_iterator.cpp b/gamgee/sam/indexed_sam_iterator.cpp
@@ -1,6 +1,7 @@
 #include "indexed_sam_iterator.h"
 #include "sam.h"
-#include "utils/hts_memory.h"
+
+#include "../utils/hts_memory.h"
 
 using namespace std;
 

diff --git a/gamgee/sam/indexed_sam_iterator.h b/gamgee/sam/indexed_sam_iterator.h
@@ -3,7 +3,7 @@
 
 #include "sam.h"
 
-#include "utils/hts_memory.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/sam.h"
 

diff --git a/gamgee/sam/indexed_sam_reader.h b/gamgee/sam/indexed_sam_reader.h
@@ -2,8 +2,9 @@
 #define gamgee__indexed_sam_reader__guard
 
 #include "indexed_sam_iterator.h"
-#include "utils/hts_memory.h"
-#include "exceptions.h"
+
+#include "../exceptions.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/sam.h"
 

diff --git a/gamgee/sam/read_bases.cpp b/gamgee/sam/read_bases.cpp
@@ -1,6 +1,7 @@
 #include "read_bases.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
+
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
 
 #include <string>
 #include <sstream>

diff --git a/gamgee/sam/sam.cpp b/gamgee/sam/sam.cpp
@@ -1,8 +1,10 @@
 #include "sam.h"
 #include "cigar.h"
-#include "utils/hts_memory.h"
+
 #include "htslib/sam.h"
-#include "missing.h"
+
+#include "../missing.h"
+#include "../utils/hts_memory.h"
 
 #include <iostream>
 #include <string>

diff --git a/gamgee/sam/sam_builder.cpp b/gamgee/sam/sam_builder.cpp
@@ -1,6 +1,7 @@
 #include "sam_builder.h"
 #include "cigar.h"
-#include "utils/hts_memory.h"
+
+#include "../utils/hts_memory.h"
 
 #include <algorithm>
 #include <sstream>

diff --git a/gamgee/sam/sam_header.cpp b/gamgee/sam/sam_header.cpp
@@ -1,5 +1,6 @@
 #include "sam_header.h"
-#include "utils/hts_memory.h"
+
+#include "../utils/hts_memory.h"
 
 using namespace std;
 

diff --git a/gamgee/sam/sam_iterator.cpp b/gamgee/sam/sam_iterator.cpp
@@ -1,6 +1,7 @@
 #include "sam_iterator.h"
 #include "sam.h"
-#include "utils/hts_memory.h"
+
+#include "../utils/hts_memory.h"
 
 using namespace std;
 

diff --git a/gamgee/sam/sam_pair_iterator.cpp b/gamgee/sam/sam_pair_iterator.cpp
@@ -1,6 +1,7 @@
 #include "sam_pair_iterator.h"
 #include "sam.h"
-#include "utils/hts_memory.h"
+
+#include "../utils/hts_memory.h"
 
 #include "htslib/sam.h"
 

diff --git a/gamgee/sam/sam_reader.h b/gamgee/sam/sam_reader.h
@@ -3,8 +3,9 @@
 
 #include "sam_iterator.h"
 #include "sam_pair_iterator.h"
-#include "utils/hts_memory.h"
-#include "exceptions.h"
+
+#include "../exceptions.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/sam.h"
 

diff --git a/gamgee/sam/sam_writer.cpp b/gamgee/sam/sam_writer.cpp
@@ -1,6 +1,6 @@
 #include "sam_writer.h"
 
-#include "utils/hts_memory.h"
+#include "../utils/hts_memory.h"
 
 namespace gamgee {
 

diff --git a/gamgee/sam/sam_writer.h b/gamgee/sam/sam_writer.h
@@ -7,7 +7,7 @@
 #include "sam.h"
 #include "sam_header.h"
 
-#include "utils/hts_memory.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/sam.h"
 

diff --git a/gamgee/utils/genotype_utils.h b/gamgee/utils/genotype_utils.h
@@ -4,6 +4,7 @@
 #include "hts_memory.h"
 #include "utils.h"
 #include "variant_field_type.h"
+
 #include "../missing.h"
 
 #include "htslib/vcf.h"

diff --git a/gamgee/utils/merged_vcf_lut.h b/gamgee/utils/merged_vcf_lut.h
@@ -1,13 +1,13 @@
 #ifndef __gamgee_merged_vcf_lut__
 #define __gamgee_merged_vcf_lut__
 
-#include<assert.h>
+#include <assert.h>
+#include <vector>
 
 #include "htslib/vcf.h"
-#include <vector>
-#include "../variant/variant_header.h"
-#include "../missing.h"
 
+#include "../missing.h"
+#include "../variant/variant_header.h"
 
 //forward declaration for friend function of MergedVCFLUTBase
 template<bool inputs_2_merged_LUT_is_input_ordered, bool merged_2_inputs_LUT_is_input_ordered>

diff --git a/gamgee/utils/variant_utils.cpp b/gamgee/utils/variant_utils.cpp
@@ -1,8 +1,9 @@
 #include "variant_utils.h"
 
-#include "../exceptions.h"
 #include "hts_memory.h"
 
+#include "../exceptions.h"
+
 #include "htslib/vcf.h"
 
 #include <algorithm>

diff --git a/gamgee/variant/genotype.h b/gamgee/variant/genotype.h
@@ -1,14 +1,14 @@
 #ifndef gamgee__genotype__guard
 #define gamgee__genotype__guard
 
-#include "utils/variant_utils.h"
-
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
-#include "utils/variant_field_type.h"
-#include "utils/genotype_utils.h"
 #include "variant_builder_multi_sample_vector.h"
 
+#include "../utils/genotype_utils.h"
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
+#include "../utils/variant_field_type.h"
+#include "../utils/variant_utils.h"
+
 #include <memory>
 #include <utility>
 #include <stdexcept>

diff --git a/gamgee/variant/indexed_variant_iterator.h b/gamgee/variant/indexed_variant_iterator.h
@@ -3,7 +3,7 @@
 
 #include "variant_iterator.h"
 
-#include "utils/hts_memory.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/indexed_variant_reader.h b/gamgee/variant/indexed_variant_reader.h
@@ -2,8 +2,9 @@
 #define gamgee__indexed_variant_reader__guard
 
 #include "indexed_variant_iterator.h"
-#include "utils/hts_memory.h"
-#include "exceptions.h"
+
+#include "../exceptions.h"
+#include "../utils/hts_memory.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/individual_field.h b/gamgee/variant/individual_field.h
@@ -4,8 +4,9 @@
 #include <iostream>
 
 #include "individual_field_iterator.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
+
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/individual_field_iterator.h b/gamgee/variant/individual_field_iterator.h
@@ -1,7 +1,7 @@
 #ifndef gamgee__individual_field_iterator__guard
 #define gamgee__individual_field_iterator__guard 
 
-#include "utils/utils.h"
+#include "../utils/utils.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/individual_field_value.h b/gamgee/variant/individual_field_value.h
@@ -2,10 +2,11 @@
 #define gamgee__individual_field_value__guard
 
 #include "individual_field_value_iterator.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
-#include "utils/variant_field_type.h"
-#include "missing.h"
+
+#include "../missing.h"
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
+#include "../utils/variant_field_type.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/individual_field_value_iterator.h b/gamgee/variant/individual_field_value_iterator.h
@@ -1,7 +1,7 @@
 #ifndef gamgee__individual_field_value_iterator__guard
 #define gamgee__individual_field_value_iterator__guard
 
-#include "utils/variant_field_type.h"
+#include "../utils/variant_field_type.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/multiple_variant_reader.h b/gamgee/variant/multiple_variant_reader.h
@@ -4,11 +4,12 @@
 #include "htslib/vcf.h"
 
 #include "variant_header.h"
-#include "utils/hts_memory.h"
-#include "utils/variant_utils.h"
-#include "exceptions.h"
 #include "variant_header_merger.h"
 
+#include "../exceptions.h"
+#include "../utils/hts_memory.h"
+#include "../utils/variant_utils.h"
+
 namespace gamgee {
 
 /**

diff --git a/gamgee/variant/shared_field.h b/gamgee/variant/shared_field.h
@@ -2,7 +2,8 @@
 #define gamgee__shared_field__guard
 
 #include "shared_field_iterator.h"
-#include "utils/utils.h"
+
+#include "../utils/utils.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/shared_field_iterator.h b/gamgee/variant/shared_field_iterator.h
@@ -1,7 +1,7 @@
 #ifndef gamgee__shared_field_iterator__guard
 #define gamgee__shared_field_iterator__guard
 
-#include "utils/variant_field_type.h"
+#include "../utils/variant_field_type.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/synced_variant_reader.h b/gamgee/variant/synced_variant_reader.h
@@ -4,8 +4,8 @@
 #include "htslib/vcf.h"
 #include "htslib/synced_bcf_reader.h"
 
-#include "exceptions.h"
-#include "utils/hts_memory.h"
+#include "../exceptions.h"
+#include "../utils/hts_memory.h"
 
 #include <string>
 #include <iostream>

diff --git a/gamgee/variant/variant.cpp b/gamgee/variant/variant.cpp
@@ -2,8 +2,9 @@
 #include "individual_field.h"
 #include "individual_field_value.h"
 #include "shared_field.h"
-#include "utils/hts_memory.h"
-#include "utils/utils.h"
+
+#include "../utils/hts_memory.h"
+#include "../utils/utils.h"
 
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/variant.h b/gamgee/variant/variant.h
@@ -7,7 +7,8 @@
 #include "shared_field.h"
 #include "variant_filters.h"
 #include "genotype.h"
-#include "utils/variant_utils.h"
+
+#include "../utils/variant_utils.h"
 
 #include "htslib/sam.h"
 #include "boost/dynamic_bitset.hpp"

diff --git a/gamgee/variant/variant_builder.cpp b/gamgee/variant/variant_builder.cpp
@@ -1,5 +1,6 @@
 #include "variant_builder.h"
-#include "missing.h"
+
+#include "../missing.h"
 
 #include <algorithm>
 #include <stdexcept>

diff --git a/gamgee/variant/variant_builder_individual_field.h b/gamgee/variant/variant_builder_individual_field.h
@@ -1,11 +1,12 @@
 #ifndef gamgee__variant_builder_individual_field__guard
 #define gamgee__variant_builder_individual_field__guard
 
-#include "utils/hts_memory.h"
-#include "utils/short_value_optimized_storage.h"
 #include "htslib/kstring.h"
 #include "htslib/vcf.h"
-#include "missing.h"
+
+#include "../missing.h"
+#include "../utils/hts_memory.h"
+#include "../utils/short_value_optimized_storage.h"
 
 #include <string>
 #include <vector>

diff --git a/gamgee/variant/variant_builder_individual_region.h b/gamgee/variant/variant_builder_individual_region.h
@@ -3,6 +3,7 @@
 
 #include "variant.h"
 #include "variant_builder_individual_field.h"
+
 #include "htslib/kstring.h"
 #include "htslib/vcf.h"
 

diff --git a/gamgee/variant/variant_builder_shared_region.cpp b/gamgee/variant/variant_builder_shared_region.cpp
@@ -1,5 +1,6 @@
 #include "variant_builder_shared_region.h"
-#include "missing.h"
+
+#include "../missing.h"
 
 #include <algorithm>
 #include <stdexcept>

diff --git a/gamgee/variant/variant_builder_shared_region.h b/gamgee/variant/variant_builder_shared_region.h
@@ -1,9 +1,11 @@
 #ifndef gamgee__variant_builder_shared_region__guard
 #define gamgee__variant_builder_shared_region__guard
 
-#include "utils/hts_memory.h"
+#include "../utils/hts_memory.h"
+
 #include "htslib/kstring.h"
 #include "htslib/vcf.h"
+
 #include "variant.h"
 
 #include <string>