SHORE API
|
shore | |
algo | |
2dex.hpp | Create and query range index files |
align.hpp | Simple dynamic programming alignment |
d2tree.hpp | 2-dimensional kd-tree |
sort_file.hpp | Low level text file sorting and merging functions |
suffix.hpp | Suffix array algorithms |
suffix_index.hpp | Suffix array on disk |
base | |
mathops.hpp | Miscellaneous math functions |
memops.hpp | Miscellaneous helpers dealing with memmory access and allocation |
pathops.hpp | Helpers dealing with file system paths |
stringops.hpp | String conversion and manipulation |
umask.hpp | |
util.hpp | Miscellaneous system utilities and other small helper functions |
container | |
frag_vector.hpp | Pseudo container combining a set of iterator ranges |
helpers.hpp | Container-related helper functions |
intpack.hpp | Unaligned integer storage |
rle_queue.hpp | Run length encoded deque |
datatype | |
alignment_processing.hpp | Read alignment processing elements |
alignment_string_ops.hpp | SHORE alignment string handling facilites |
aminoacid.hpp | Amino acids |
coor.hpp | Reference sequence coordinates |
datatypes.hpp | SHORE data records |
dna_iterator.hpp | Iterate over DNA sequences in different encodings |
nucleotide.hpp | Nucleotides |
read_processing.hpp | Raw read processing elements |
serialization.hpp | Libboost_serialization compliant serialization functions for libshore datatypes |
fmtio | |
alignment.hpp | File format independent short read alignment reader |
aln.hpp | Cisgenome ALN file IO |
bed.hpp | BED file IO |
eland.hpp | ELAND alignment file IO |
fasta.hpp | FastA file IO |
fastq.hpp | FastQ file IO |
flatread.hpp | SHORE FlatRead format file IO |
gff.hpp | GFF file IO |
maplist.hpp | SHORE MapList file IO |
mummer.hpp | MUMmer delta file IO |
psl.hpp | BLAT PSL / PSLX file IO |
qseq.hpp | Illumina QSEQ read file format IO |
read.hpp | File format independent short read file reader |
refdict.hpp | |
sam.hpp | SAM/BAM file IO |
segment.hpp | Read genomic segments in various file formats |
sff.hpp | 454 SFF file IO |
text.hpp | ASCII plain text file IO |
vcf.hpp | Currently just quality_variant -> VCF conversion |
parallel | |
message_passing.hpp | Interface to the Message Passing Interface |
message_passing_proxy.hpp | Message passing interface parallelization proxy |
parallel.hpp | Memory sharing agnostic parallelization system |
parallel_log.hpp | Mutually exclusive log file access |
thread.hpp | Thread class |
thread_index.hpp | Thread ID management |
processing | |
buffer_chain.hpp | Integrate plain data sources with an internal buffer |
extractor.hpp | Retrieve data from a pipeline |
feed.hpp | Feed data to a pipeline |
filter.hpp | Connect file readers, writers and processing steps through a signal/slot pipeline system |
merge.hpp | Merge data from multiple pipeline inputs |
method_check.hpp | Check for presence of the optional pipeline methods flush(), next(), prepare() |
monolithic_source.hpp | Integrate plain data sources with an internal buffer |
pipe_box.hpp | Template for transforming pipe elements for stand-alone use |
pipeline.hpp | Connect file readers, writers and processing steps through a signal/slot pipeline system |
plugin.hpp | Integrate plain data sources with an internal buffer |
signalslot.hpp | Signal/slot system |
program | |
av_parser.hpp | Command line option parser |
program.hpp | Program base class file |
uncaught_handler.hpp | Handle program exceptions |
statistics | |
berry.hpp | Finding the optimal log-transformation constant for ANOVA-type models uing the method proposed by Berry |
binomial.hpp | Binomial distribution |
chisquare.hpp | Chi square distribution |
exponential.hpp | Exponential distribution |
geometric.hpp | Geometric distribution |
glm.hpp | General Linear Model and linear hypothesis test |
mtc.hpp | Implements the multiple testing correction methods of R's multtest package |
poisson.hpp | Poisson distribution |
stream | |
fileext.hpp | Helpers dealing with compression-related file extensions |
gzx.hpp | Block-wise compression in gzip format |
stream_slicer.hpp | Chop a file or input stream into slices |
streams.hpp | Stream classes |
transpose.hpp | |
xzx.hpp | Block-wise compression in xz/lzma2 format |