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C++ C Perl
tag: v0.02

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samples
t
.gitignore
Makefile
NMakefile
README
appears.cpp
ddebug.h

README

This program aims to solve the simple bioinformatical problem
presented in the following PerlChina mailing list threads:

  http://groups.google.com/group/perlchina/browse_thread/thread/a019034ad1dc584e

  http://groups.google.com/group/perlchina/browse_thread/thread/e8d38aa1a2d8d356

It should run on Win32 with Visual C++ and g++ for Linux.
Other flavors of systems should work as well, but need some tweaks
in the Makefile.

[ Win32 ]

You should have Visual C++ 2002 or better installed and have run
vcvars32.bat to set the environments required to run command-line
VC compiler "cl.exe".

To build everything:

   nmake -f NMakefile

To run the little test suite:

   nmake -f NMakefile test

The expected testing output is similar to the output of the Linux
version given below.

(Note that large files beyond 4GB have not tested on Win32.)

[ Linux ]

To build everything:

    make

To run the little test suite:

    make test

The "appear" program is for 15-char sequences, "appear2" for 2-char
sequences, and "appear1" for 1-char sequences.

The expected testing output is like:

    ./appears
    ERROR: No input file specified.
    make: [test] Error 1 (ignored)
    ===========================
    ./appears no-such-file
    ERROR: Failed to open input file no-such-file for reading: No such file or directory
    make: [test] Error 1 (ignored)
    ===========================
    ./appears samples/invalid.txt
    ERROR: File samples/invalid.txt: line 2: Invalid character found: 'D' (0x44)
    make: [test] Error 1 (ignored)
    ===========================
    ./appears2 samples/good2.txt
    INFO: Using a bit array of length 16 (sequence length: 2).
    INFO: Searching missing combinations of sequences...
      TG (index 8)
      TA (index 9)
      TT (index 10)
    For total 3 missing combinations found.
    ===========================
    ./appears1 samples/good1.txt
    INFO: Using a bit array of length 4 (sequence length: 1).
    INFO: Searching missing combinations of sequences...
      T (index 2)
    For total 1 missing combinations found.
    ===========================
    ./appears1 samples/good2.txt
    INFO: Using a bit array of length 4 (sequence length: 1).
    INFO: Searching missing combinations of sequences...
    All combinations have appeared.

-agentzh

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