gamgee/doxygen/gamgee_8h_source.html

 #ifndef gamgee__gamgee__guard

 #define gamgee__gamgee__guard


 #include "exceptions.h"

 #include "fastq.h"

 #include "fastq_iterator.h"

 #include "fastq_reader.h"

 #include "interval.h"

 #include "missing.h"

 #include "reference_iterator.h"

 #include "reference_map.h"

 #include "zip.h"


 #include "utils/file_utils.h"

 #include "utils/genotype_utils.h"

 #include "utils/hts_memory.h"

 #include "utils/merged_vcf_lut.h"

 #include "utils/short_value_optimized_storage.h"

 #include "utils/utils.h"

 #include "utils/variant_field_type.h"

 #include "utils/variant_utils.h"


 #include "sam/base_quals.h"

 #include "sam/cigar.h"

 #include "sam/indexed_sam_iterator.h"

 #include "sam/indexed_sam_reader.h"

 #include "sam/read_bases.h"

 #include "sam/sam.h"

 #include "sam/sam_builder.h"

 #include "sam/sam_builder_data_field.h"

 #include "sam/sam_header.h"

 #include "sam/sam_iterator.h"

 #include "sam/sam_pair_iterator.h"

 #include "sam/sam_reader.h"

 #include "sam/sam_tag.h"

 #include "sam/sam_writer.h"


 #include "variant/genotype.h"

 #include "variant/indexed_variant_iterator.h"

 #include "variant/indexed_variant_reader.h"

 #include "variant/individual_field.h"

 #include "variant/individual_field_iterator.h"

 #include "variant/individual_field_value.h"

 #include "variant/individual_field_value_iterator.h"

 #include "variant/multiple_variant_iterator.h"

 #include "variant/multiple_variant_reader.h"

 #include "variant/reference_block_splitting_variant_iterator.h"

 #include "variant/shared_field.h"

 #include "variant/shared_field_iterator.h"

 #include "variant/synced_variant_iterator.h"

 #include "variant/synced_variant_reader.h"

 #include "variant/variant.h"

 #include "variant/variant_builder.h"

 #include "variant/variant_builder_individual_field.h"

 #include "variant/variant_builder_individual_region.h"

 #include "variant/variant_builder_multi_sample_vector.h"

 #include "variant/variant_builder_shared_region.h"

 #include "variant/variant_filters.h"

 #include "variant/variant_filters_iterator.h"

 #include "variant/variant_header.h"

 #include "variant/variant_header_builder.h"

 #include "variant/variant_iterator.h"

 #include "variant/variant_reader.h"

 #include "variant/variant_writer.h"

 #include "variant/variant_header_merger.h"


 #endif  /* gamgee__gamgee__guard */

indexed_sam_reader.h

fastq.h

zip.h

sam_iterator.h

variant_utils.h

variant_builder_shared_region.h

shared_field.h

sam_reader.h

missing.h

variant_field_type.h

variant_builder_individual_field.h

read_bases.h

fastq_reader.h

indexed_variant_reader.h

utils.h

sam_builder_data_field.h

individual_field_iterator.h

variant.h

shared_field_iterator.h

sam_builder.h

individual_field.h

synced_variant_reader.h

variant_builder_multi_sample_vector.h

exceptions.h

file_utils.h

cigar.h

indexed_sam_iterator.h

sam.h

sam_writer.h

reference_map.h

genotype.h

variant_header_merger.h

variant_builder_individual_region.h

individual_field_value_iterator.h

indexed_variant_iterator.h

reference_iterator.h

variant_header_builder.h

sam_tag.h

short_value_optimized_storage.h

variant_filters.h

variant_writer.h

synced_variant_iterator.h

fastq_iterator.h

hts_memory.h

genotype_utils.h

merged_vcf_lut.h

multiple_variant_reader.h

reference_block_splitting_variant_iterator.h

sam_header.h

multiple_variant_iterator.h

variant_iterator.h

variant_reader.h

variant_filters_iterator.h

variant_builder.h

variant_header.h

base_quals.h

individual_field_value.h

sam_pair_iterator.h

interval.h