Files
e-PCR package includes two tool sets: forward
e-PCR (e-PCR) and reverse e-PCR (re-PCR, fahash and famap). These
binaries share some source files, that are compiled as
libepcr.a library.
Directory stand/ contains makefiles to use
with GCC. Change stand/config.mk to update compiler
and compiling options. Makefiles should be OK for GNU
make.
Sources common to forward and reverse e-PCR binaries
- build_cfg.h
- macroses that control compilation
with/without NCBI toolkit
- defaults.h
- defaults for e-PCR program (used also in library)
- mswin.h
- windows compatibility defines and declarations
- native64.h
- native 64bit file access compatibility defines and declarations
- strref.hpp
- class for passing reference to string data
- sts_i.hpp
- generic STS interface class
- hashset.hpp
- hash calculating class
declaration (allows set of discontiguos words)
- hashset.cpp
- hash calculating class
implementation
- align.hpp
- align or compare two sequences allowing
mismatches and gaps, declarations
- align.cpp
- align or compare two sequences allowing
mismatches and gaps, implementation
- minilcs.hpp
- align two sequences templat class
- faread.hpp
- read fasta files, declarations
- faread.cpp
- read fasta files, implementation
- mmap.hpp
- mmap(2) wrapper for huge files and no
page boundary restriction, declarations
- mmap.cpp
- mmap(2) wrapper for huge files and no
page boundary restriction, implementation
- getopt.c
- getopt implementation -- to compile for
windows
Forward e-PCR source files
- e-PCR_main.cpp
- main for e-PCR commandline program
- stsmatch_i.hpp
- STS lookup algorithm declarations
- stsmatch_i.cpp
- STS lookup algorithm implementation
- stsfilter.cpp
- Postprocessor for STS lookup
- stsmatch_m.hpp
- STS and STS hash table
implementation for mmapable UniSTS file, declarations
- stsmatch_m.cpp
- STS and STS hash table
implementation for mmapable UniSTS file, implementation
- stsmatch.hpp
- Some useful callbacks
declarations
- stsmatch.cpp
- Some useful callbacks,
implementation
Reverse e-PCR source files
- bin-io.hpp
- Generic read/write integers and strings
- fahash_defines.h
- Internal defines for fahash
- fahash_internal.hpp
- Internal defines for fahash
- fahash.hpp
- Hash sequence words in file, declarations
- fahash_create.cpp
- Hash sequence words in file,
creating hash file, abstract
- fahash_create1.cpp
- Hash sequence words in file,
creating hash file version 1 implementation
- fahash_create2.cpp
- Hash sequence words in file,
creating hash file version 2 implementation
- fahash_lookup.cpp
- Hash sequence words in file,
lookup algorithm implementation
- fast_seqio.hpp
- Fast access to regions of
sequences, declarations
- fast_seqio_read.cpp
- Fast access to regions of
sequences, implementation
- fast_seqio_write.cpp
- Fast access to regions of
sequences, create sequence file implementation
- famap_main.cpp
- main for commandline tool to
create/dump mmapable file
- fahash_main.cpp
- main for commandline tool to
create hash file
- sts.hpp
- simple implementation for STS class
- re-PCR_main.cpp
- main for reverse e-PCR commandline tool
Extra files
- seqcmp_main.cpp
- Main file for align.?pp
test
Build files
- Makefile
- Master makefile
- stand/version.mk
- Version definitions
- stand/config.mk
- Compiler options
- stand/Makefile.libepcr
- libepcr makefile
- stand/Makefile.cmd_epcr
- e-PCR makefile
- stand/Makefile.cmd_repcr
- re-PCR makefile
- stand/Makefile.cmd_famap
- famap makefile
- stand/Makefile.cmd_fahash
- fahash makefile
- stand/Makefile.cmd_seqcmp
- seqcmp makefile
- stand/Makefile.bcc55-w32
- makefile for BorlandC++/win32
- stand/Makefile.vc8
- makefile for MS Visual C++ 8.0