From nobody Tue Oct 12 16:43:26 2021 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 54A7217FC168; Tue, 12 Oct 2021 16:43:27 +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 4HTM1C11Frz4lFj; Tue, 12 Oct 2021 16:43:27 +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 DC5D417A77; Tue, 12 Oct 2021 16:43:26 +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 19CGhQeD031102; Tue, 12 Oct 2021 16:43:26 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 19CGhQLX031101; Tue, 12 Oct 2021 16:43:26 GMT (envelope-from git) Date: Tue, 12 Oct 2021 16:43:26 GMT Message-Id: <202110121643.19CGhQLX031101@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: cdf2ff2f68e6 - main - biology/bamutil: Utilities for working with SAM/BAM files List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org 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: cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 commit cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 Author: Jason W. Bacon AuthorDate: 2021-10-12 16:40:35 +0000 Commit: Jason W. Bacon CommitDate: 2021-10-12 16:40:35 +0000 biology/bamutil: Utilities for working with SAM/BAM files Utilities for working on SAM/BAM files from The Center for Statistical Genetics at the University of Michigan School of Public Health. It includes numerous functions such as splitting, merging, trimming reads, filtering, validation, diff, etc. --- biology/Makefile | 1 + biology/bamutil/Makefile | 26 ++++++++++++++++++++++ biology/bamutil/distinfo | 5 +++++ .../files/patch-libStatGen_Makefiles_Makefile.lib | 17 ++++++++++++++ .../patch-libStatGen_Makefiles_Makefile.toolchain | 13 +++++++++++ .../patch-libStatGen_vcf_VcfRecordGenotype.cpp | 11 +++++++++ biology/bamutil/pkg-descr | 6 +++++ 7 files changed, 79 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index ba430926041c..c779368ef1d2 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -6,6 +6,7 @@ SUBDIR += avida SUBDIR += babel SUBDIR += bamtools + SUBDIR += bamutil SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools diff --git a/biology/bamutil/Makefile b/biology/bamutil/Makefile new file mode 100644 index 000000000000..1df27f50678d --- /dev/null +++ b/biology/bamutil/Makefile @@ -0,0 +1,26 @@ +PORTNAME= bamutil +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.14 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utilities for working with SAM/BAM files + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/copyrights/COPYING + +USES= gmake +USE_GITHUB= yes + +GH_ACCOUNT= statgen +GH_PROJECT= bamUtil + +# Build needs access to libStatGen Makefiles, so can't install separately +GH_TUPLE= statgen:libStatGen:v${DISTVERSION}:statgen/libStatGen + +MAKE_ENV= LIB_PATH_GENERAL=${WRKSRC}/libStatGen +MAKE_ENV+= INSTALLDIR=${STAGEDIR}${PREFIX}/bin + +PLIST_FILES= bin/bam + +.include diff --git a/biology/bamutil/distinfo b/biology/bamutil/distinfo new file mode 100644 index 000000000000..4f76b5616521 --- /dev/null +++ b/biology/bamutil/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1634051641 +SHA256 (statgen-bamUtil-v1.0.14_GH0.tar.gz) = f5ec8d5e98a3797742106c3413a4ab1622d8787e38b29b3df4cddb59d77efda5 +SIZE (statgen-bamUtil-v1.0.14_GH0.tar.gz) = 1916953 +SHA256 (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b +SIZE (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 558924 diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib new file mode 100644 index 000000000000..7f8d5a434e94 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib @@ -0,0 +1,17 @@ +--- libStatGen/Makefiles/Makefile.lib.orig 2021-10-12 15:28:34 UTC ++++ libStatGen/Makefiles/Makefile.lib +@@ -34,11 +34,11 @@ profile: $(STAT_GEN_LIB_PROFILE) + # To build the library, build the objects + # Then add them to the library + $(STAT_GEN_LIB_OPT): $(OBJECTS_OPT) +- ar -cru $@ $(OBJECTS_OPT) ++ ar -cr $@ $(OBJECTS_OPT) + $(STAT_GEN_LIB_DEBUG): $(OBJECTS_DEBUG) +- ar -cru $@ $(OBJECTS_DEBUG) ++ ar -cr $@ $(OBJECTS_DEBUG) + $(STAT_GEN_LIB_PROFILE): $(OBJECTS_PROFILE) +- ar -cru $@ $(OBJECTS_PROFILE) ++ ar -cr $@ $(OBJECTS_PROFILE) + + UNAME=$(shell uname) + diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain new file mode 100644 index 000000000000..447be2125380 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain @@ -0,0 +1,13 @@ +--- libStatGen/Makefiles/Makefile.toolchain.orig 2021-10-12 15:09:29 UTC ++++ libStatGen/Makefiles/Makefile.toolchain +@@ -51,8 +51,8 @@ endif + + # CPP0X=-std=c++0x + +-CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X) +-CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc ++CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)c++ $(CPP0X) ++CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cc + LD = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld + AR = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar + RANLIB = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib diff --git a/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp b/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp new file mode 100644 index 000000000000..db31c78ab9d7 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp @@ -0,0 +1,11 @@ +--- libStatGen/vcf/VcfRecordGenotype.cpp.orig 2021-10-12 15:13:03 UTC ++++ libStatGen/vcf/VcfRecordGenotype.cpp +@@ -176,7 +176,7 @@ bool VcfRecordGenotype::setString(const std::string& k + if(sampleNum >= mySamples.size()) + { + // Out of range sample index. +- return(NULL); ++ return(false); + } + // Set the field in the sample. + return(mySamples.get(sampleNum).setString(key, value)); diff --git a/biology/bamutil/pkg-descr b/biology/bamutil/pkg-descr new file mode 100644 index 000000000000..6eb44e52fcb7 --- /dev/null +++ b/biology/bamutil/pkg-descr @@ -0,0 +1,6 @@ +Utilities for working on SAM/BAM files from The Center for Statistical +Genetics at the University of Michigan School of Public Health. It +includes numerous functions such as splitting, merging, trimming reads, +filtering, validation, diff, etc. + +WWW: https://github.com/statgen/bamUtil