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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