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Viewing changes to src/sequence/sequence_io.h

Committer: Package Import Robot
Author(s): Andreas Tille
Date: 2014-02-13 13:57:55 UTC
Revision ID: package-import@ubuntu.com-20140213135755-c97jpl9wl5yzfwfw

Tags: upstream-1.1.1

Import upstream version 1.1.1

files added:

AUTHORS

ChangeLog

Makefile.am

Makefile.in

NEWS

README

aclocal.m4

bin/Makefile.am

bin/Makefile.in

config.h.in

configure

configure.ac

depcomp

install-sh

lib/Makefile.am

lib/Makefile.in

missing

script

script/Makefile.am

script/Makefile.in

script/run-unittest.py

script/scan.py

script/validate_blat

script/validate_blat_parallel

src/assembly

src/assembly/assembly_utility.cpp

src/assembly/assembly_utility.h

src/assembly/local_assembler.cpp

src/assembly/local_assembler.h

src/basic

src/basic/atomic_integer.h

src/basic/bit_operation.h

src/basic/functional.h

src/basic/hash.h

src/basic/histgram.h

src/basic/kmer.h

src/basic/math.cpp

src/basic/math.h

src/basic/pool.h

src/container

src/container/hash_map.h

src/container/hash_set.h

src/container/hash_table.h

src/container/managed_list.h

src/graph

src/graph/bit_edges.h

src/graph/contig_builder.h

src/graph/contig_graph.cpp

src/graph/contig_graph.h

src/graph/contig_graph_branch_group.cpp

src/graph/contig_graph_branch_group.h

src/graph/contig_graph_path.h

src/graph/contig_graph_vertex.h

src/graph/contig_info.cpp

src/graph/contig_info.h

src/graph/hash_graph.cpp

src/graph/hash_graph.h

src/graph/hash_graph_branch_group.cpp

src/graph/hash_graph_branch_group.h

src/graph/hash_graph_path.h

src/graph/hash_graph_vertex.h

src/graph/scaffold_graph.cpp

src/graph/scaffold_graph.h

src/graph/scaffold_graph_path.h

src/graph/scaffold_graph_vertex.h

src/graph/vertex_status.h

src/misc

src/misc/blat_record.cpp

src/misc/blat_record.h

src/misc/hash_aligner.cpp

src/misc/hash_aligner.h

src/misc/log.cpp

src/misc/log.h

src/misc/options_description.cpp

src/misc/options_description.h

src/misc/utils.cpp

src/misc/utils.h

src/release

src/release/filterfa.cpp

src/release/fq2fa.cpp

src/release/idba.cpp

src/release/idba_hybrid.cpp

src/release/idba_tran.cpp

src/release/idba_ud.cpp

src/release/parallel_blat.cpp

src/release/raw_n50.cpp

src/release/sim_reads.cpp

src/release/sim_reads_tran.cpp

src/release/split_scaffold.cpp

src/release/validate_contigs_blat.cpp

src/sequence

src/sequence/compact_sequence.cpp

src/sequence/compact_sequence.h

src/sequence/read_library.h

src/sequence/sequence.cpp

src/sequence/sequence.h

src/sequence/sequence_io.cpp

src/sequence/sequence_io.h

src/sequence/sequence_reader.cpp

src/sequence/sequence_reader.h

src/sequence/sequence_writer.cpp

src/sequence/sequence_writer.h

src/sequence/short_sequence.cpp

src/sequence/short_sequence.h

src/tools

src/tools/fa2fq.cpp

src/tools/filter_blat.cpp

src/tools/filter_contigs.cpp

src/tools/idba_tran_test.cpp

src/tools/parallel_rna_blat.cpp

src/tools/print_graph.cpp

src/tools/sample_reads.cpp

src/tools/scaffold.cpp

src/tools/shuffle_reads.cpp

src/tools/sort_psl.cpp

src/tools/sort_reads.cpp

src/tools/split_fa.cpp

src/tools/split_fq.cpp

src/tools/test.cpp

src/tools/validate_component.cpp

src/tools/validate_contigs_mummer.cpp

src/tools/validate_reads_blat.cpp

src/tools/validate_rna.cpp

test

test/Makefile.am

test/Makefile.in

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src/sequence/sequence_io.h

/**

* @file sequence_io.h

* @brief Useful functions for sequence I/O.

* @author Yu Peng (ypeng@cs.hku.hk)

* @version 1.0.0

* @date 2011-08-06

#ifndef __SEQUENCE_SEQUENCE_IO_H_

#define __SEQUENCE_SEQUENCE_IO_H_

#include <stdint.h>

#include <string>

#include <deque>

#include "sequence/sequence_reader.h"

#include "sequence/sequence_writer.h"

class Sequence;

class ShortSequence;

class FastaWriter;

class ShortReadLibrary;

class LongReadLibrary;

uint64_t ReadLibrary(const std::string &filename, ShortReadLibrary &library);

uint64_t ReadLibrary(const std::string &filename, LongReadLibrary &library);

uint64_t ReadSequence(const std::string &filename, std::deque<Sequence> &sequences);

uint64_t ReadSequence(const std::string &filename, std::deque<Sequence> &sequences, std::deque<std::string> &names);

uint64_t ReadSequence(const std::string &filename, std::deque<ShortSequence> &sequences);

uint64_t ReadSequence(const std::string &filename, std::deque<ShortSequence> &sequences, std::deque<std::string> &names);

uint64_t WriteSequence(const std::string &filename, const std::deque<Sequence> &sequences, const std::string &prefix = "");

uint64_t WriteSequence(FastaWriter &writer, const std::deque<Sequence> &sequences, const std::string &prefix = "");

uint64_t WriteSequence(const std::string &filename, const std::deque<ShortSequence> &sequences, const std::string &prefix = "");

uint64_t WriteSequence(FastaWriter &writer, const std::deque<ShortSequence> &sequences, const std::string &prefix = "");

#endif

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