Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/blasr blasr-2015.08.17 as wip/ blasr.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 15:12:27 2016 -0500
Changeset:	61916e531c051cb937c72dc44211cdba6468e1ae

Added Files:
	blasr/DESCR
	blasr/Makefile
	blasr/PLIST
	blasr/TODO
	blasr/buildlink3.mk
	blasr/distinfo
	blasr/patches/patch-Blasr.cpp

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/blasr
blasr-2015.08.17 as wip/blasr.

PacBio(R) long read aligner.

WWW: https://github.com/PacificBiosciences/blasr

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=61916e531c051cb937c72dc44211cdba6468e1ae

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 blasr/DESCR                   |  3 ++
 blasr/Makefile                | 69 +++++++++++++++++++++++++++++++++++++++++++
 blasr/PLIST                   | 10 +++++++
 blasr/TODO                    |  1 +
 blasr/buildlink3.mk           | 12 ++++++++
 blasr/distinfo                |  7 +++++
 blasr/patches/patch-Blasr.cpp | 21 +++++++++++++
 7 files changed, 123 insertions(+)

diffs:
diff --git a/blasr/DESCR b/blasr/DESCR
new file mode 100644
index 0000000..a3f8db8
--- /dev/null
+++ b/blasr/DESCR
@@ -0,0 +1,3 @@
+PacBio(R) long read aligner.
+
+WWW: https://github.com/PacificBiosciences/blasr
diff --git a/blasr/Makefile b/blasr/Makefile
new file mode 100644
index 0000000..e3f2efe
--- /dev/null
+++ b/blasr/Makefile
@@ -0,0 +1,69 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+DISTNAME=	blasr-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX=	.tar.xz
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	PacBio(R) long read aligner
+# Double-check this
+LICENSE=	modified-bsd
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+SUBST_CLASSES+=		bash
+SUBST_STAGE.bash=	post-patch
+SUBST_FILES.bash=	${WRKSRC}/makefile
+SUBST_SED.bash=		-e 's|/bin/bash|${PREFIX}/bin/bash|g'
+SUBST_SED.bash+=	-e 's|-ldl||g'
+
+SUBST_CLASSES+=		libs
+SUBST_STAGE.libs=	post-configure
+SUBST_FILES.libs=	${WRKSRC}/defines.mk
+SUBST_SED.libs=		-e 's|-ldl||g'
+SUBST_SED.libs+=	-e 's|-static||g'
+
+CXXFLAGS+=	-I${PREFIX}/include/blasr_libcpp \
+		-I${PREFIX}/include/blasr_libcpp/hdf \
+		-I${PREFIX}/include/blasr_libcpp/pbdata \
+		-I${PREFIX}/include/blasr_libcpp/alignment \
+		-I${PREFIX}/include
+MAKE_FILE=	makefile
+
+PORTVERSION=	2015.08.17
+
+AUTO_MKDIRS=	yes
+
+do-configure:
+	cd ${WRKSRC} && ./configure.py --no-pbbam \
+		NOPBBAM=1 HDF5_INCLUDE=${PREFIX}/include \
+		HDF5_LIB=${PREFIX}/lib
+
+do-install:
+	${INSTALL_PROGRAM} \
+		${WRKSRC}/blasr \
+		${WRKSRC}/utils/loadPulses \
+		${WRKSRC}/utils/pls2fasta \
+		${WRKSRC}/utils/samFilter \
+		${WRKSRC}/utils/samtoh5 \
+		${WRKSRC}/utils/samtom4 \
+		${WRKSRC}/utils/sawriter \
+		${WRKSRC}/utils/sdpMatcher \
+		${WRKSRC}/utils/toAfg \
+		${DESTDIR}${PREFIX}/bin
+
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../devel/hdf5-c++/buildlink3.mk"
+.include "../../wip/blasr_libcpp/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/blasr/PLIST b/blasr/PLIST
new file mode 100644
index 0000000..75b72a0
--- /dev/null
+++ b/blasr/PLIST
@@ -0,0 +1,10 @@
+@comment $NetBSD$
+bin/blasr
+bin/loadPulses
+bin/pls2fasta
+bin/samFilter
+bin/samtoh5
+bin/samtom4
+bin/sawriter
+bin/sdpMatcher
+bin/toAfg
diff --git a/blasr/TODO b/blasr/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/blasr/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/blasr/buildlink3.mk b/blasr/buildlink3.mk
new file mode 100644
index 0000000..2920513
--- /dev/null
+++ b/blasr/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	blasr
+
+.if !defined(BLASR_BUILDLINK3_MK)
+BLASR_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.blasr+=	blasr>=2015.08.17
+BUILDLINK_PKGSRCDIR.blasr?=	../../wip/blasr
+.endif	# BLASR_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-blasr
diff --git a/blasr/distinfo b/blasr/distinfo
new file mode 100644
index 0000000..86c4281
--- /dev/null
+++ b/blasr/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (blasr-2015.08.17.tar.xz) = fd89eac035087b7a41295e7c6b20b678266628b4
+RMD160 (blasr-2015.08.17.tar.xz) = d85998bc824b6ad3319e140478d86b8ac6ffb056
+SHA512 (blasr-2015.08.17.tar.xz) = dcb3e9df039a09862bc25b9d4b9120e65bae7c8f3d7f38a81db21a8687c86d50ecacf32640af13ea8dfbd1b8d6adf198e7f58b3cc7b38022f1552e37046eb81d
+Size (blasr-2015.08.17.tar.xz) = 1027344 bytes
+SHA1 (patch-Blasr.cpp) = 663437d839027a7a6f057cf44234a96f6eb7299c
diff --git a/blasr/patches/patch-Blasr.cpp b/blasr/patches/patch-Blasr.cpp
new file mode 100644
index 0000000..7025346
--- /dev/null
+++ b/blasr/patches/patch-Blasr.cpp
@@ -0,0 +1,21 @@
+$NetBSD$
+# Replce C++11ism
+
+--- Blasr.cpp.orig	2015-08-13 20:42:14.000000000 +0000
++++ Blasr.cpp
+@@ -2655,9 +2655,12 @@ SelectAlignmentsToPrint(vector<T_Alignme
+   // Apply filter criteria and hit policy.
+   // Shallow copy AlignmentCandidate pointers.
+   vector<T_AlignmentCandidate*> filtered;
+-  for (auto ptr: alignmentPtrs) {
+-      if (params.filterCriteria.Satisfy(ptr)) {
+-          filtered.push_back(ptr);
++  // for (auto ptr: alignmentPtrs) {
++  //    if (params.filterCriteria.Satisfy(ptr)) {
++  //        filtered.push_back(ptr);
++  for (int i = 0; i < alignmentPtrs.size(); ++i) {
++      if (params.filterCriteria.Satisfy(alignmentPtrs[i])) {
++          filtered.push_back(alignmentPtrs[i]);
+           if (filtered.size() == params.nBest) break;
+       }
+   }