From owner-dev-commits-ports-main@freebsd.org Tue Sep 7 20:33:41 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 18AE766B3ED; Tue, 7 Sep 2021 20:33:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4H3xn103WDz3pZV; Tue, 7 Sep 2021 20:33:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id D6A3A190DF; Tue, 7 Sep 2021 20:33:40 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 187KXehv069868; Tue, 7 Sep 2021 20:33:40 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 187KXeop069867; Tue, 7 Sep 2021 20:33:40 GMT (envelope-from git) Date: Tue, 7 Sep 2021 20:33:40 GMT Message-Id: <202109072033.187KXeop069867@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: e61df5e46475 - main - biology/sam2pairwise: Show pairwise alignment for each read in a SAM file MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e61df5e464758cb1d460c95b4fbb3855a4f7f6dc Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 07 Sep 2021 20:33:41 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e61df5e464758cb1d460c95b4fbb3855a4f7f6dc commit e61df5e464758cb1d460c95b4fbb3855a4f7f6dc Author: Jason W. Bacon AuthorDate: 2021-09-07 20:32:29 +0000 Commit: Jason W. Bacon CommitDate: 2021-09-07 20:32:29 +0000 biology/sam2pairwise: Show pairwise alignment for each read in a SAM file sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read. --- biology/Makefile | 1 + biology/sam2pairwise/Makefile | 20 ++++++++++++++++ biology/sam2pairwise/distinfo | 3 +++ biology/sam2pairwise/files/patch-Makefile | 39 +++++++++++++++++++++++++++++++ biology/sam2pairwise/pkg-descr | 4 ++++ 5 files changed, 67 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index f97c311da9fe..294a87ca4e78 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -171,6 +171,7 @@ SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell + SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview diff --git a/biology/sam2pairwise/Makefile b/biology/sam2pairwise/Makefile new file mode 100644 index 000000000000..dd578353e5a9 --- /dev/null +++ b/biology/sam2pairwise/Makefile @@ -0,0 +1,20 @@ +PORTNAME= sam2pairwise +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Show pairwise alignment for each read in a SAM file + +LICENSE= MIT +LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/LICENSE + +USE_GITHUB= yes + +GH_ACCOUNT= mlafave + +WRKSRC_SUBDIR= src +ALL_TARGET= sam2pairwise +PLIST_FILES= bin/sam2pairwise + +.include diff --git a/biology/sam2pairwise/distinfo b/biology/sam2pairwise/distinfo new file mode 100644 index 000000000000..364e6c8bde7c --- /dev/null +++ b/biology/sam2pairwise/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1631041315 +SHA256 (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 899d3db071cc248870bbedbdb39784de4c54c9a7888bc408022e809ace47ec0e +SIZE (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 10013 diff --git a/biology/sam2pairwise/files/patch-Makefile b/biology/sam2pairwise/files/patch-Makefile new file mode 100644 index 000000000000..56ed56b8a857 --- /dev/null +++ b/biology/sam2pairwise/files/patch-Makefile @@ -0,0 +1,39 @@ +--- Makefile.orig 2014-08-22 20:02:24 UTC ++++ Makefile +@@ -1,8 +1,19 @@ +-CXX = g++ +-CC = g++ ++CXX ?= g++ ++LD = ${CXX} + +-sam2pairwise: sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o translate_cigar.o translate_md.o ++OBJS = sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o \ ++ translate_cigar.o translate_md.o + ++PREFIX ?= /usr/local ++DESTDIR ?= . ++INSTALL ?= install ++MKDIR ?= mkdir ++ ++all: sam2pairwise ++ ++sam2pairwise: ${OBJS} ++ ${CXX} ${OBJS} -o sam2pairwise ++ + isolate_md.o: isolate_md.cc isolate_md.hh + + shift_cigar.o: shift_cigar.cc shift_cigar.hh +@@ -15,6 +26,11 @@ translate_md.o: translate_md.cc translate_md.hh + + sam2pairwise.o: sam2pairwise.cc isolate_md.hh shift_cigar.hh shift_md.hh translate_cigar.hh translate_md.hh + +-clobber: +- rm -f *.o core sam2pairwise ++.PHONY: install clean + ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c sam2pairwise ${DESTDIR}${PREFIX}/bin ++ ++clean: ++ rm -f *.o core sam2pairwise diff --git a/biology/sam2pairwise/pkg-descr b/biology/sam2pairwise/pkg-descr new file mode 100644 index 000000000000..800de1d7998e --- /dev/null +++ b/biology/sam2pairwise/pkg-descr @@ -0,0 +1,4 @@ +sam2pairwise takes a SAM file and uses the CIGAR and MD tag to +reconstruct the pairwise alignment of each read. + +WWW: https://github.com/mlafave/sam2pairwise