File: Changes

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epcr 2.3.12-1-9
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file content (135 lines) | stat: -rw-r--r-- 3,909 bytes parent folder | download | duplicates (6)
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version		 2.3.12
affected:	 few *.cpp files
description:
	- Added include of cstdio to make it compilable with gcc 4.4 (thanks to Ubuntu and 
	  Debian-med teams)

version		 2.3.11
affected:    stsmatch_i.?pp
description: 
	- When parsing commandline if -d was used before -w or -f default size was reset to 
	  program's default

version		 2.3.10
affected:	 includes in a few files
description:
	- Applied user-provided patch to add includes for gcc-4.3 compatibility

version		 2.3.9
affected:    fahash_lookup.cpp
description: 
	- Fixed a bug leading to false negatives when run without optimization

version		 2.3.8
affected:	 e-PCR_main.cpp build_cfg.h 
added:		 ncbi/Makefile ncbi/Makefile.INCLUDE
description:
	- Added possibility to compile with NCBI C++ toolkit and read blastdb instead of fasta

version		 2.3.7
affected:	 build_cfg.h fast_seqio*.?pp fahash*.?pp stsmatch_m.cpp
description:
	- Fixed reverse e-pcr code to work on Linux 64 bit architecture

version      2.3.6
added:		 stand/Makefile.vc8
affected:	 mswin.h *_main.cpp
description:
	- Fixed some warnings and made it compileable by MS Visual C++ 8.0

affected:	 
version		 2.3.5
affected:	 fahash_create2.cpp
description:
	- Made more details to report seek failure 

version		 2.3.4
affected:    re-PCR_main.cpp, fahash_main.cpp
description: 
	- Minor changes to progress reporting

version      2.3.3
affected:    e-PCR_main.cpp (forward e-PCR) output
description:
        - Attention: Hit positions do not include floppy tails anymore
        - TODO: same with reverse e-PCR
		- Fixed typo in BUILD.*

version      2.3.2
affected:    stsmatch_i.?pp, e-PCR_main.cpp (forward e-PCR)
description:
        - Progress indication is more detailed and controlled

version      2.3.1
affected:    sts_i.hpp, stsmatch_m.?pp (forward e-PCR)
description:
	- Bugfix: some hits were lost with large margin
	- Bugfix: re-PCR for win32 now works again
	- Can read primers from file

version      2.3.0
affected:    sts_i.hpp, stsmatch_m.?pp (forward e-PCR)
description:
        - Support for overhang nucleotides in primers as masked characters

version      2.2.3
affected:    Makefiles
description:
	- Compiling under Mac OS X

version      2.2.2
affected:    API, re-PCR, e-PCR, commandline
description:
	- Better consistency for misalignments found and alignments shown

version      2.2.1
affected:    API, re-PCR, commandline
description:
	- New output for re-PCR is available (with alignments)

version      2.2.0
affected:    Building, API, data format, e-PCR, re-PCR, commandline
description:
	- API: Alignment now is performed by IAlign interface
	- seqcmp class is obsolete
	- Added new alignment method, more presize but slow (fixes bug)
	- New output is available, with graphic representation of alignments

version      2.1.0
affected:    Building, API, data format, e-PCR, commandline
description: 
        - e-PCR, re-PCR: fixed bug, that forbidded overlapping primers
        - e-PCR        : fixed `empty description is shown as to "?"'
        - re-PCR       : hash file version 2, new build algorithm
                         new "fahash" program generates hash files
                         re-PCR is for lookup only


version      2.0.5
affected:    Building, e-PCR, famap, commandline
description: All tools are working for windows. Fasta conversion is added.


version      2.0.4
affected:    Building
description: Now compileable with Borlang C++ Builder 5.5 for win32


version      2.0.3
affected:    commandline parsing, API, defaults
description: Changed defaults for M (Margin); now can be changed from 
	     commandline


version      2.0.2
affected:    e-PCR commandline parsing
description: Fixed commandline processing -- compat options are allowed
	     anywhere


version      2.0.1
affected:    API
description: independent report for left and right primer misalignments
             in forward e-pcr API