Date: Sat, 21 Jun 2008 00:01:57 +0000 (UTC) From: Felippe de Meirelles Motta <lippe@FreeBSD.org> To: ports-committers@FreeBSD.org, cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org Subject: cvs commit: ports/biology Makefile ports/biology/ssaha Makefile distinfo pkg-descr pkg-plist ports/biology/ssaha/files patch-GlobalDefinitions.cpp patch-GlobalDefinitions.h patch-HashTable.cpp patch-HashTableGeneric.cpp patch-HashTablePacked.cpp patch-HashTablePacked.h ... Message-ID: <200806210001.m5L01vHj017020@repoman.freebsd.org>
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lippe 2008-06-21 00:01:57 UTC
FreeBSD ports repository
Modified files:
biology Makefile
Added files:
biology/ssaha Makefile distinfo pkg-descr pkg-plist
biology/ssaha/files patch-GlobalDefinitions.cpp
patch-GlobalDefinitions.h
patch-HashTable.cpp
patch-HashTableGeneric.cpp
patch-HashTablePacked.cpp
patch-HashTablePacked.h
patch-HashTableTranslated.cpp
patch-MatchAligner.cpp
patch-MatchAligner.h patch-MatchStore.h
patch-MatchStoreGapped.h
patch-MatchStoreUngapped.h
patch-QueryManager.cpp
patch-QueryManager.h patch-README
patch-SSAHAMain.cpp patch-SSAHAMain.h
patch-SequenceEncoder.cpp
patch-SequenceReader.cpp
patch-SequenceReader.h
patch-SequenceReaderFasta.cpp
patch-SequenceReaderFasta.h
patch-SequenceReaderFilter.h
patch-SequenceReaderLocal.cpp
patch-SequenceReaderMulti.cpp
patch-SequenceReaderMulti.h
patch-SequenceReaderString.h
patch-makefile
patch-testHashTableNoOverlap.cpp
patch-testQueryManager.cpp
patch-testSequenceReaderFasta.cpp
Log:
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/
PR: ports/124525
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by: gabor (mentor, implicit)
Revision Changes Path
1.102 +1 -0 ports/biology/Makefile
1.1 +33 -0 ports/biology/ssaha/Makefile (new)
1.1 +3 -0 ports/biology/ssaha/distinfo (new)
1.1 +11 -0 ports/biology/ssaha/files/patch-GlobalDefinitions.cpp (new)
1.1 +82 -0 ports/biology/ssaha/files/patch-GlobalDefinitions.h (new)
1.1 +20 -0 ports/biology/ssaha/files/patch-HashTable.cpp (new)
1.1 +48 -0 ports/biology/ssaha/files/patch-HashTableGeneric.cpp (new)
1.1 +29 -0 ports/biology/ssaha/files/patch-HashTablePacked.cpp (new)
1.1 +16 -0 ports/biology/ssaha/files/patch-HashTablePacked.h (new)
1.1 +77 -0 ports/biology/ssaha/files/patch-HashTableTranslated.cpp (new)
1.1 +94 -0 ports/biology/ssaha/files/patch-MatchAligner.cpp (new)
1.1 +33 -0 ports/biology/ssaha/files/patch-MatchAligner.h (new)
1.1 +54 -0 ports/biology/ssaha/files/patch-MatchStore.h (new)
1.1 +25 -0 ports/biology/ssaha/files/patch-MatchStoreGapped.h (new)
1.1 +13 -0 ports/biology/ssaha/files/patch-MatchStoreUngapped.h (new)
1.1 +54 -0 ports/biology/ssaha/files/patch-QueryManager.cpp (new)
1.1 +19 -0 ports/biology/ssaha/files/patch-QueryManager.h (new)
1.1 +13 -0 ports/biology/ssaha/files/patch-README (new)
1.1 +48 -0 ports/biology/ssaha/files/patch-SSAHAMain.cpp (new)
1.1 +19 -0 ports/biology/ssaha/files/patch-SSAHAMain.h (new)
1.1 +75 -0 ports/biology/ssaha/files/patch-SequenceEncoder.cpp (new)
1.1 +20 -0 ports/biology/ssaha/files/patch-SequenceReader.cpp (new)
1.1 +11 -0 ports/biology/ssaha/files/patch-SequenceReader.h (new)
1.1 +32 -0 ports/biology/ssaha/files/patch-SequenceReaderFasta.cpp (new)
1.1 +11 -0 ports/biology/ssaha/files/patch-SequenceReaderFasta.h (new)
1.1 +20 -0 ports/biology/ssaha/files/patch-SequenceReaderFilter.h (new)
1.1 +28 -0 ports/biology/ssaha/files/patch-SequenceReaderLocal.cpp (new)
1.1 +30 -0 ports/biology/ssaha/files/patch-SequenceReaderMulti.cpp (new)
1.1 +13 -0 ports/biology/ssaha/files/patch-SequenceReaderMulti.h (new)
1.1 +26 -0 ports/biology/ssaha/files/patch-SequenceReaderString.h (new)
1.1 +15 -0 ports/biology/ssaha/files/patch-makefile (new)
1.1 +178 -0 ports/biology/ssaha/files/patch-testHashTableNoOverlap.cpp (new)
1.1 +20 -0 ports/biology/ssaha/files/patch-testQueryManager.cpp (new)
1.1 +171 -0 ports/biology/ssaha/files/patch-testSequenceReaderFasta.cpp (new)
1.1 +11 -0 ports/biology/ssaha/pkg-descr (new)
1.1 +9 -0 ports/biology/ssaha/pkg-plist (new)
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