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C++ C Perl
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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