From owner-cvs-ports@FreeBSD.ORG Sat Jun 21 00:01:58 2008 Return-Path: Delivered-To: cvs-ports@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id F3928106567B; Sat, 21 Jun 2008 00:01:57 +0000 (UTC) (envelope-from lippe@FreeBSD.org) Received: from repoman.freebsd.org (repoman.freebsd.org [IPv6:2001:4f8:fff6::29]) by mx1.freebsd.org (Postfix) with ESMTP id CE16A8FC18; Sat, 21 Jun 2008 00:01:57 +0000 (UTC) (envelope-from lippe@FreeBSD.org) Received: from repoman.freebsd.org (localhost [127.0.0.1]) by repoman.freebsd.org (8.14.1/8.14.1) with ESMTP id m5L01vOQ017021; Sat, 21 Jun 2008 00:01:57 GMT (envelope-from lippe@repoman.freebsd.org) Received: (from lippe@localhost) by repoman.freebsd.org (8.14.1/8.14.1/Submit) id m5L01vHj017020; Sat, 21 Jun 2008 00:01:57 GMT (envelope-from lippe) Message-Id: <200806210001.m5L01vHj017020@repoman.freebsd.org> From: Felippe de Meirelles Motta Date: Sat, 21 Jun 2008 00:01:57 +0000 (UTC) To: ports-committers@FreeBSD.org, cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org X-FreeBSD-CVS-Branch: HEAD Cc: 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 ... X-BeenThere: cvs-ports@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: CVS commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 21 Jun 2008 00:01:58 -0000 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 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)