File List

Here is a list of all files with brief descriptions:

[detail level 1234567]

▼ build
► CMakeFiles
► 3.1.0-rc1
► CompilerIdC
CMakeCCompilerId.c
► CompilerIdCXX
CMakeCXXCompilerId.cpp
feature_tests.c
feature_tests.cxx
► contrib
► htslib
► src
► htslib
► cram
cram.h
cram_codecs.c
cram_codecs.h
cram_decode.c
cram_decode.h
cram_encode.c
cram_encode.h
cram_index.c
cram_index.h
cram_io.c
cram_io.h
cram_samtools.c
cram_samtools.h
cram_stats.c
cram_stats.h
cram_structs.h
files.c
md5.c
md5.h
mFILE.c
mFILE.h
misc.h
open_trace_file.c
open_trace_file.h
os.h
pooled_alloc.c
pooled_alloc.h
rANS_byte.h
rANS_static.c
rANS_static.h
sam_header.c
sam_header.h
string_alloc.c
string_alloc.h
thread_pool.c
thread_pool.h
vlen.c
vlen.h
zfio.c
zfio.h
► htslib
bgzf.h
faidx.h
hfile.h
hts.h
hts_defs.h
kfunc.h
khash.h
khash_str2int.h
klist.h
knetfile.h
kseq.h
ksort.h
kstring.h
regidx.h
sam.h
synced_bcf_reader.h
tbx.h
vcf.h
vcf_sweep.h
vcfutils.h
► test
fieldarith.c
hfile.c
sam.c
test-regidx.c
test-vcf-api.c
test-vcf-sweep.c
test_view.c
bgzf.c
bgzip.c
config.h
faidx.c
hfile.c
hfile_internal.h
hfile_net.c
hts.c
htsfile.c
kfunc.c
knetfile.c
kstring.c
regidx.c
sam.c
synced_bcf_reader.c
tabix.c
tbx.c
vcf.c
vcf_sweep.c
vcfutils.c
version.h
▼ gamgee
► sam
base_quals.cpp
base_quals.h
cigar.cpp
cigar.h
indexed_sam_iterator.cpp
indexed_sam_iterator.h
indexed_sam_reader.h
read_bases.cpp
read_bases.h
read_group.cpp
read_group.h
sam.cpp
sam.h
sam_builder.cpp
sam_builder.h
sam_builder_data_field.cpp
sam_builder_data_field.h
sam_header.cpp
sam_header.h
sam_iterator.cpp
sam_iterator.h
sam_pair_iterator.cpp
sam_pair_iterator.h
sam_reader.h
sam_tag.h
sam_writer.cpp
sam_writer.h
► utils
file_utils.cpp
file_utils.h
genotype_utils.cpp
genotype_utils.h
hts_memory.cpp
hts_memory.h
merged_vcf_lut.cpp
merged_vcf_lut.h
short_value_optimized_storage.h
utils.cpp
utils.h
variant_field_type.cpp
variant_field_type.h
variant_utils.cpp
variant_utils.h
► variant
genotype.cpp
genotype.h
indexed_variant_iterator.cpp
indexed_variant_iterator.h
indexed_variant_reader.h
individual_field.h
individual_field_iterator.h
individual_field_value.h
individual_field_value_iterator.h
multiple_variant_iterator.cpp
multiple_variant_iterator.h
multiple_variant_reader.h
reference_block_splitting_variant_iterator.cpp
reference_block_splitting_variant_iterator.h
shared_field.h
shared_field_iterator.h
synced_variant_iterator.cpp
synced_variant_iterator.h
synced_variant_reader.h
variant.cpp
variant.h
variant_builder.cpp
variant_builder.h
variant_builder_individual_field.h
variant_builder_individual_region.cpp
variant_builder_individual_region.h
variant_builder_multi_sample_vector.h
variant_builder_shared_region.cpp
variant_builder_shared_region.h
variant_filters.h
variant_filters_iterator.h
variant_header.cpp
variant_header.h
variant_header_builder.cpp
variant_header_builder.h
variant_header_merger.cpp
variant_header_merger.h
variant_iterator.cpp
variant_iterator.h
variant_reader.h
variant_writer.cpp
variant_writer.h
exceptions.h
fastq.cpp
fastq.h
fastq_iterator.cpp
fastq_iterator.h
fastq_reader.cpp
fastq_reader.h
gamgee.h
interval.cpp
interval.h
missing.h
reference_iterator.cpp
reference_iterator.h
reference_map.cpp
reference_map.h
zip.h