File: BUILD.txt

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             Electronic PCR commandline tools: build instructions

                                                          Version: 2.3.12
     _________________________________________________________________

   Build e-PCR and reverse e-PCR (re-PCR, famap) binaries with GNU make
   and GCC.
     _________________________________________________________________

Build

Unix/gcc instructions

    1. Unpack archive
    2. Edit stand/config.mk if nesessary
    3. run gmake links depend all OPTIMIZE=6

Make arguments

   One can use following arguments to make:

   OPTIMIZE=[0-9]
          to pass with -O argument to compiler (default is build debug
          version)

   srcdir={path-to-src}
          to set path to sources

   objdir={path-to-obj}
          to set path where to place .o

   tgtdir={target-path}
          to set path where to put targets (libepcr.a and executable
          files)

Mac OS/X with gcc

   Use LF64LDFLAGS= LF64CCFLAGS=-DNATIVE_LARGEFILES (yes, space after
   first "=") argument with gmake since Mac OS/2 does not have (and does
   not need) *64 file functions and off64_t

Windows/BorlandC++ instructions

    1. Unpack archive
    2. Edit stand/Makefile.bcc55-w32 if nesessary
    3. run make all -f stand/Makefile.bcc55-w32

Windows/MS-VisualC++8.0 instructions

    1. Unpack archive
    2. Edit stand/Makefile.vc8 if nesessary
    3. run nmake all -f stand/Makefile.vc8
     _________________________________________________________________

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
     _________________________________________________________________