File List

Here is a list of all files with brief descriptions:

[detail level 12345]

contrib
bamtools
BamAux.h
BamReader.cpp
BamReader.h
BamWriter.cpp
BamWriter.h
BGZF.cpp
BGZF.h
crc
crc.cpp
crc.h
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
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
kstdint.h
kstring.h
sam.h
synced_bcf_reader.h
tbx.h
vcf.h
vcf_sweep.h
vcfutils.h
bgzf.c
bgzip.c
config.h
faidx.c
hfile.c
hfile_internal.h
hfile_net.c
hts.c
kfunc.c
knetfile.c
kstring.c
sam.c
synced_bcf_reader.c
tabix.c
tbx.c
vcf.c
vcf_sweep.c
vcfutils.c
version.h
libdivsufsort-lite
divsufsort.c
divsufsort.h
suftest.c
libdivsufsortxx
divsufsortxx.h
lz4
lz4.c
lz4.h
lz4frame.c
lz4frame.h
lz4frame_static.h
lz4hc.c
lz4hc.h
xxhash.c
xxhash.h
moderngpu
include
util
format.h
mgpualloc.h
mgpucontext.h
static.h
util.h
mgpuenums.h
mmio.h
sparsematrix.h
src
mgpuutil.cpp
mmio.cpp
sparsematrix.cpp
priority-deque
interval_heap.hpp
main.cpp
priority_deque.hpp
priority_deque_verify.hpp
zlib
zconf.h
zlib.h
zlib-1.2.7
adler32.c
compress.c
crc32.c
crc32.h
deflate.c
deflate.h
gzclose.c
gzguts.h
gzlib.c
gzread.c
gzwrite.c
infback.c
inffast.c
inffast.h
inffixed.h
inflate.c
inflate.h
inftrees.c
inftrees.h
trees.c
trees.h
uncompr.c
zlib.h
zutil.c
zutil.h
sais.h
contrib
zlib-1.2.7
zconf.h
examples
fmmap
util.h
qmap
alignment.h
util.h
vsam
util.h
nvbio
alignment
ed
ed_banded_inl.h
ed_inl.h
ed_utils.h
ed_warp_inl.h
gotoh
gotoh_banded_inl.h
gotoh_inl.h
gotoh_warp_inl.h
hamming
hamming_inl.h
myers
myers_banded_inl.h
sw
sw_banded_inl.h
sw_inl.h
sw_warp_inl.h
alignment.h
alignment_base.h
alignment_base_inl.h
alignment_inl.h
banded_inl.h
batched.h
batched_banded_inl.h
batched_inl.h
batched_stream.h
sink.h
sink_inl.h
utils.h
utils_inl.h
warp_utils.h
basic
cuda
arch.h
arch_inl.h
atomics.h
condition.h
host_device_buffer.h
ldg.h
pingpong_queues.h
primitives.h
primitives_inl.h
scan.h	Define CUDA based scan primitives
simd_functions.h
sort.h	Define CUDA based sort primitives
syncblocks.h
syncblocks_inl.h
tex.h
timer.h
work_queue.h
work_queue_inl.h
work_queue_multipass.h
work_queue_multipass_inl.h
work_queue_ordered.h
work_queue_ordered_inl.h
work_queue_persistent.h
work_queue_persistent_inl.h
algorithms.h	Defines some general purpose algorithms
atomics.cpp
atomics.h
bloom_filter.h
bloom_filter_inl.h
bnt.cpp
bnt.h
cache.h
cache_inl.h
cached_iterator.h	CUDA-compatible iterator wrappers allowing to cache the dereferenced value of generic iterators
cached_iterator_inl.h
cast_iterator.h
console.cpp
console.h
deinterleaved_iterator.h
dna.h
exceptions.cpp
exceptions.h
html.cpp
html.h
index_transform_iterator.h
interval_heap.h
iterator.h
iterator_reference.h
merge_sort.h
mmap.cpp
mmap.h
numbers.h
omp.h
options.h
packed_vector.h
packed_vector_inl.h
packedstream.h
packedstream_inl.h
packedstream_loader.h
packedstream_loader_inl.h
pipeline.h
pipeline_context.h
pipeline_inl.h
pod.h
popcount.h
popcount_inl.h
primitives.h
primitives_inl.h
priority_deque.h
priority_queue.h	A CUDA-compatible, fixed-size priority queue
priority_queue_inline.h
profiling.h
shared_pointer.h
simd.h
simd_inl.h
static_vector.h
static_vector_inl.h
strided_iterator.h
sum_tree.h
sum_tree_inl.h
system.cpp
system.h
threads.cpp
threads.h
thrust_view.h
timer.cpp
timer.h
transform_iterator.h
types.h
vector.h	Define host / device vectors
vector_array.h
vector_loads.h
vector_view.h
version.h
fasta
fasta.h
fasta_inl.h
fastq
fastq.cpp
fastq.h
fastq_inl.h
fmindex
backtrack.h
bidir.h
bidir_inl.h
bwt.h
filter.h
filter_inl.h
fmindex.h
fmindex_device.h
fmindex_inl.h
mem.h
mem_inl.h
paged_text.cpp
paged_text.h
paged_text_inl.h
rank_dictionary.h
rank_dictionary_inl.h
ssa.h
ssa_inl.h
io
fmindex
fmindex.h
output
output_bam.cpp
output_bam.h
output_batch.cpp
output_batch.h
output_databuffer.cpp
output_databuffer.h
output_debug.cpp
output_debug.h
output_file.cpp
output_file.h
output_gzip.cpp
output_gzip.h
output_priv.cpp
output_priv.h
output_sam.cpp
output_sam.h
output_stats.cpp
output_stats.h
output_types.h
output_utils.h
reads
bam.cpp
bam.h
reads.cpp
reads.h
reads_fastq.cpp
reads_fastq.h
reads_priv.h
reads_txt.cpp
reads_txt.h
sam.cpp
sam.h
sequence
sequence.h
sequence_access.h
sequence_bam.cpp
sequence_bam.h
sequence_encoder.cpp
sequence_encoder.h
sequence_fasta.cpp
sequence_fasta.h
sequence_fastq.cpp
sequence_fastq.h
sequence_mmap.cpp
sequence_mmap.h
sequence_pac.cpp
sequence_pac.h
sequence_priv.cpp
sequence_priv.h
sequence_sam.cpp
sequence_sam.h
sequence_traits.h
sequence_txt.cpp
sequence_txt.h
alignments.h
alignments_inl.h
bam_format.h
bufferedtextfile.h
output_stream.cpp
output_stream.h
utils.h
vcf.cpp
vcf.h
qgram
filter.h
filter_inl.h
qgram.h
qgram_inl.h
qgroup.h
qgroup_inl.h
strings
alphabet.h
alphabet_inl.h
infix.h
prefetcher.h
prefix.h
seeds.h
seeds_inl.h
string.h
string_iterator.h	Generic string iterator, which can be used to build an iterator for any string container
string_iterator_inl.h
string_set.h
string_set_inl.h
string_set_transform.h
string_traits.h
suffix.h
vectorized_string.h
wavelet_tree.h
wavelet_tree_inl.h
sufsort
blockwise_sufsort.h
bwte.h
bwte_inl.h
compression_sort.h
dcs.h
dcs_inl.h
file_bwt.h
file_bwt_bgz.h
file_bwt_lz4.h
prefix_doubling_sufsort.h
sufsort.h
sufsort_bucketing.h
sufsort_inl.h
sufsort_priv.h
sufsort_utils.h
trie
sorted_dictionary.h
sorted_dictionary_inl.h
suffix_trie.h
suffix_trie_inl.h
nvbio-aln-diff
alignment.cpp
alignment.h
alignment_bam.cpp
alignment_dbg.cpp
filter.h
html.h
nvbio-aln-diff.cpp
pe_analyzer.cpp
pe_analyzer.h
se_analyzer.cpp
se_analyzer.h
stats.h
utils.h
nvbio-test
alignment_test_utils.h
bwt_test.cpp
cache_test.cpp
fasta_test.cpp
fastq_test.cpp
nvbio-test.cpp
packedstream_test.cpp
sum_tree_test.cpp
utils.h
nvBowtie
bowtie2
cuda
aligner.h
aligner_all.h
aligner_best_approx.h
aligner_best_approx_paired.h
aligner_best_exact.h
aligner_inst.h
alignment_utils.h
checksums.h
compute_thread.h
defs.h
fmindex_def.h
func.h
input_thread.cpp
input_thread.h
locate.h
locate_inl.h
mapping.h
mapping_impl.h
mapping_inl.h
mapq.cpp
mapq.h
params.cpp
params.h
persist.h
pipeline_states.h
reads_def.h
reduce.h
reduce_impl.h
reduce_inl.h
score.h
score_all_impl.h
score_all_inl.h
score_best_impl.h
score_best_inl.h
score_opposite_impl.h
score_opposite_inl.h
score_paired_impl.h
score_paired_inl.h
scoring.h
scoring_inl.h
scoring_queues.h
scoring_queues_inl.h
seed_hit.h
seed_hit_deque_array.h
seed_hit_deque_array_inl.h
select.h
select_impl.h
select_inl.h
stats.cpp
stats.h
string_utils.h
traceback.h
traceback_impl.h
traceback_inl.h
utils.h
quality_coeffs.cpp
quality_coeffs.h
nvBowtie.cpp
nvBWT
filelist.cpp
filelist.h
nvFM-server
nvFM-server.cpp
nvLighter
bloom_filters.h
error_correct.h
input_thread.h
output_thread.h
sample_kmers.h
utils.h
nvMicroAssembly
assembly.h
assembly_graph.h
assembly_graph_inl.h
assembly_types.h
bam_io.h
haplotype_caller.h
kmers.h
kmers_inl.h
regions.h
nvSetBWT
input_thread.h
nvSSA
nvSSA.cpp
sw-benchmark
ssw.cpp
ssw.h
vs
nvbio-less
nvbio-less.cpp
sse-test
cpu.cpp
simd_functions.h
sse_cuda.h
zlib
zconf.h
zlib.h
proposal.h