hisat2: Update to 2.2.1

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: hisat2: Update to 2.2.1
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Wed, 16 Mar 2022 21:06:07 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Mar 16 16:06:07 2022 -0500
Changeset:	339dbf6d193bfaee20397e06ba436059ff4b8ff2

Modified Files:
	hisat2/Makefile
	hisat2/PLIST
	hisat2/distinfo
	hisat2/patches/patch-hisat2
Added Files:
	hisat2/patches/patch-Makefile
	hisat2/patches/patch-aligner__sw.h
	hisat2/patches/patch-processor__support.h
	hisat2/patches/patch-sse__util.h
Removed Files:
	hisat2/files/Makefile.pkg

Log Message:
hisat2: Update to 2.2.1

Also import SIMDe patches from FreeBSD (disabled until SIMDe is ported)

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=339dbf6d193bfaee20397e06ba436059ff4b8ff2

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

diffstat:
 hisat2/Makefile                           |  15 +-
 hisat2/PLIST                              |  27 +-
 hisat2/distinfo                           |  12 +-
 hisat2/files/Makefile.pkg                 | 443 ------------------------------
 hisat2/patches/patch-Makefile             |  84 ++++++
 hisat2/patches/patch-aligner__sw.h        |  22 ++
 hisat2/patches/patch-hisat2               |   2 +-
 hisat2/patches/patch-processor__support.h |  25 ++
 hisat2/patches/patch-sse__util.h          |  22 ++
 9 files changed, 175 insertions(+), 477 deletions(-)

diffs:
diff --git a/hisat2/Makefile b/hisat2/Makefile
index 324b6329a4..a08cb41c61 100644
--- a/hisat2/Makefile
+++ b/hisat2/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD$
 
-DISTNAME=	hisat2-2.1.0.23
+DISTNAME=	hisat2-v2.2.1
+PKGNAME=	hisat2-2.2.1
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=infphilo/}
-GITHUB_TAG=	20f333e2cfe7ff4d1362b248912893e2644683d7
+MASTER_SITES=	${MASTER_SITE_GITHUB:=DaehwanKimLab/}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://ccb.jhu.edu/software/hisat2/index.shtml
@@ -16,13 +16,12 @@ ONLY_FOR_PLATFORM=	*-*-x86_64
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	bash gmake perl
 
-REPLACE_BASH=		hisatgenotype_scripts/*.sh
-REPLACE_PERL=		hisat2 scripts/*.sh scripts/*.pl
-REPLACE_PYTHON=		*.py hisat2-build hisat2-inspect
-REPLACE_PYTHON+=	hisatgenotype_modules/*.py hisatgenotype_scripts/*.py
+REPLACE_BASH=		scripts/*.sh
+REPLACE_PERL=		hisat2 scripts/*.sh scripts/*.pl scripts/*.py
+REPLACE_PYTHON=		*.py scripts/*.py hisat2-build hisat2-inspect
 
-MAKE_FILE=		${FILESDIR}/Makefile.pkg
 PTHREAD_AUTO_VARS=	yes
+WRKSRC=			${WRKDIR}/hisat2-2.2.1
 
 .include "../../lang/python/application.mk"
 .include "../../mk/pthread.buildlink3.mk"
diff --git a/hisat2/PLIST b/hisat2/PLIST
index d85cbf8bd5..96055d08a6 100644
--- a/hisat2/PLIST
+++ b/hisat2/PLIST
@@ -8,9 +8,8 @@ bin/hisat2-build-s
 bin/hisat2-inspect
 bin/hisat2-inspect-l
 bin/hisat2-inspect-s
-libexec/hisat2/compare_HLA_Omixon.py
+bin/hisat2-repeat
 libexec/hisat2/convert_quals.pl
-libexec/hisat2/extract_Omixon_HLA.py
 libexec/hisat2/extract_exons.py
 libexec/hisat2/extract_splice_sites.py
 libexec/hisat2/gen_2b_occ_lookup.pl
@@ -20,21 +19,8 @@ libexec/hisat2/hisat2_extract_exons.py
 libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
 libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
 libexec/hisat2/hisat2_extract_splice_sites.py
+libexec/hisat2/hisat2_read_statistics.py
 libexec/hisat2/hisat2_simulate_reads.py
-libexec/hisat2/hisatgenotype.py
-libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py
-libexec/hisat2/hisatgenotype_assembly_graph.py
-libexec/hisat2/hisatgenotype_build_genome.py
-libexec/hisat2/hisatgenotype_convert_codis.py
-libexec/hisat2/hisatgenotype_extract_codis_data.py
-libexec/hisat2/hisatgenotype_extract_cyp_data.py
-libexec/hisat2/hisatgenotype_extract_reads.py
-libexec/hisat2/hisatgenotype_extract_vars.py
-libexec/hisat2/hisatgenotype_gene_typing.py
-libexec/hisat2/hisatgenotype_hla_cyp.py
-libexec/hisat2/hisatgenotype_locus.py
-libexec/hisat2/hisatgenotype_locus_samples.py
-libexec/hisat2/hisatgenotype_typing_common.py
 libexec/hisat2/infer_fraglen.pl
 libexec/hisat2/make_a_thaliana_tair.sh
 libexec/hisat2/make_b_taurus_UMD3.sh
@@ -50,7 +36,9 @@ libexec/hisat2/make_grch37_snp_tran.sh
 libexec/hisat2/make_grch37_snp_tran_ercc.sh
 libexec/hisat2/make_grch37_tran.sh
 libexec/hisat2/make_grch38.sh
+libexec/hisat2/make_grch38_rep.sh
 libexec/hisat2/make_grch38_snp.sh
+libexec/hisat2/make_grch38_snp_rep.sh
 libexec/hisat2/make_grch38_snp_tran.sh
 libexec/hisat2/make_grch38_snp_tran_ercc.sh
 libexec/hisat2/make_grch38_tran.sh
@@ -75,8 +63,5 @@ libexec/hisat2/make_sc3.sh
 libexec/hisat2/make_wbcel235.sh
 libexec/hisat2/make_wbcel235_tran.sh
 libexec/hisat2/make_zm3_snp_tran_ercc.sh
-libexec/hisat2/run_extract_CP.sh
-libexec/hisat2/run_extract_ILMN.sh
-libexec/hisat2/run_genotype_build.sh
-libexec/hisat2/run_hisat2_build.sh
-libexec/hisat2/run_type_CP.sh
+libexec/hisat2/sa.py
+libexec/hisat2/validate_repeat.py
diff --git a/hisat2/distinfo b/hisat2/distinfo
index 5488d89fb2..5982988e81 100644
--- a/hisat2/distinfo
+++ b/hisat2/distinfo
@@ -1,6 +1,10 @@
 $NetBSD$
 
-RMD160 (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 71f956d15b7d6d610a71a7026baa89115224b359
-SHA512 (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 5514f7462a6738e5fed5ef3bd2eb782e867178cd68eb36324407628b446a151d096326d859b2986877a26206ad182281ecac29f2abd01991c0640c5e4c5e5e0b
-Size (hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz) = 3975385 bytes
-SHA1 (patch-hisat2) = ea55c8a99dcd2fd3651e832fbb402b94d0ea3fed
+BLAKE2s (hisat2-v2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb
+SHA512 (hisat2-v2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
+Size (hisat2-v2.2.1.tar.gz) = 6761242 bytes
+SHA1 (patch-Makefile) = e002806f8daa4e5c45b95b5f173de818a8737b43
+SHA1 (patch-aligner__sw.h) = bdd7e3a189b5c2886df85cc4252d4f41487f423f
+SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
+SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af
+SHA1 (patch-sse__util.h) = c1dd6bc593a14ef5617e1d67e211a2e7a96a6022
diff --git a/hisat2/files/Makefile.pkg b/hisat2/files/Makefile.pkg
deleted file mode 100644
index c70690ac2e..0000000000
--- a/hisat2/files/Makefile.pkg
+++ /dev/null
@@ -1,443 +0,0 @@
-#
-# Generic Makefile for package managers
-# J Bacon <bacon4000%gmail.com@localhost>
-#
-# This Makefile respects standard make variables provided by package
-# managers, such as CXX, CXXFLAGS, etc.  It is intended to work on
-# any POSIX platform.  Default behaviour should be similar to the
-# original Makefile.
-#
-# This file is part of HISAT2.
-#
-# HISAT 2 is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# HISAT 2 is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with HISAT.  If not, see <http://www.gnu.org/licenses/>.
-#
-
-INC =
-GCC_PREFIX = $(shell dirname `which gcc`)
-GCC_SUFFIX =
-
-CC	?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP	?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-CXX	?= $(CPP)
-CXXFLAGS ?= -O2 -Wall
-INSTALL	?= install
-
-HEADERS = $(wildcard *.h)
-BOWTIE_MM = 1
-BOWTIE_SHARED_MEM = 0
-
-MACOS = 0
-ifneq (,$(findstring Darwin,$(shell uname)))
-	MACOS = 1
-endif
-
-# EXTRA_FLAGS += -DPOPCNT_CAPABILITY
-INC += -I third_party
-
-MM_DEF = 
-
-ifeq (1,$(BOWTIE_MM))
-	MM_DEF = -DBOWTIE_MM
-endif
-
-SHMEM_DEF = 
-
-ifeq (1,$(BOWTIE_SHARED_MEM))
-	SHMEM_DEF = -DBOWTIE_SHARED_MEM
-endif
-
-SEARCH_LIBS = 
-BUILD_LIBS = 
-INSPECT_LIBS =
-
-USE_SRA = 0
-SRA_DEF =
-SRA_LIB =
-SERACH_INC = 
-ifeq (1,$(USE_SRA))
-	SRA_DEF = -DUSE_SRA
-	SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
-	SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
-	SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
-endif
-
-LIBS = $(LDFLAGS)
-
-SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
-	edit.cpp gfm.cpp \
-	reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
-	random_source.cpp tinythread.cpp
-SEARCH_CPPS = qual.cpp pat.cpp \
-	read_qseq.cpp aligner_seed_policy.cpp \
-	aligner_seed.cpp \
-	aligner_seed2.cpp \
-	aligner_sw.cpp \
-	aligner_sw_driver.cpp aligner_cache.cpp \
-	aligner_result.cpp ref_coord.cpp mask.cpp \
-	pe.cpp aln_sink.cpp dp_framer.cpp \
-	scoring.cpp presets.cpp unique.cpp \
-	simple_func.cpp \
-	random_util.cpp \
-	aligner_bt.cpp sse_util.cpp \
-	aligner_swsse.cpp outq.cpp \
-	aligner_swsse_loc_i16.cpp \
-	aligner_swsse_ee_i16.cpp \
-	aligner_swsse_loc_u8.cpp \
-	aligner_swsse_ee_u8.cpp \
-	aligner_driver.cpp \
-	splice_site.cpp 
-
-SEARCH_OBJS = qual.o pat.o \
-	read_qseq.o aligner_seed_policy.o \
-	aligner_seed.o \
-	aligner_seed2.o \
-	aligner_sw.o \
-	aligner_sw_driver.o aligner_cache.o \
-	aligner_result.o ref_coord.o mask.o \
-	pe.o aln_sink.o dp_framer.o \
-	scoring.o presets.o unique.o \
-	simple_func.o \
-	random_util.o \
-	aligner_bt.o sse_util.o \
-	aligner_swsse.o outq.o \
-	aligner_swsse_loc_i16.o \
-	aligner_swsse_ee_i16.o \
-	aligner_swsse_loc_u8.o \
-	aligner_swsse_ee_u8.o \
-	aligner_driver.o \
-	splice_site.o 
-
-BUILD_CPPS = diff_sample.cpp
-
-HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
-HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
-
-SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
-VERSION = $(shell cat VERSION)
-
-DEBUG_FLAGS    = $(CXXFLAGS) -O0 -g3
-DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS  = $(CXXFLAGS)
-RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
-NOASSERT_FLAGS = -DNDEBUG
-FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-
-ifeq (1,$(USE_SRA))
-	ifeq (1, $(MACOS))
-		DEBUG_FLAGS += -mmacosx-version-min=10.6
-		RELEASE_FLAGS += -mmacosx-version-min=10.6
-	endif
-endif
-
-
-HISAT2_BIN_LIST = hisat2-build-s \
-	hisat2-build-l \
-	hisat2-align-s \
-	hisat2-align-l \
-	hisat2-inspect-s \
-	hisat2-inspect-l
-HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \
-	hisat2-build-l-debug \
-	hisat2-align-s-debug \
-	hisat2-align-l-debug \
-	hisat2-inspect-s-debug \
-	hisat2-inspect-l-debug
-
-GENERAL_LIST = $(wildcard scripts/*.sh) \
-	$(wildcard scripts/*.pl) \
-	$(wildcard *.py) \
-	$(wildcard hisatgenotype_modules/*.py) \
-	$(wildcard hisatgenotype_scripts/*.py) \
-	doc/manual.inc.html \
-	doc/README \
-	doc/style.css \
-	$(wildcard example/index/*.ht2) \
-	$(wildcard example/reads/*.fa) \
-	example/reference/22_20-21M.fa \
-	example/reference/22_20-21M.snp \
-	$(PTHREAD_PKG) \
-	hisat2 \
-	hisat2-build \
-	hisat2-inspect \
-	AUTHORS \
-	LICENSE \
-	NEWS \
-	MANUAL \
-	MANUAL.markdown \
-	TUTORIAL \
-	VERSION
-
-ifeq (1,$(WINDOWS))
-	HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
-endif
-
-# This is helpful on Windows under MinGW/MSYS, where Make might go for
-# the Windows FIND tool instead.
-FIND=$(shell which find)
-
-SRC_PKG_LIST = $(wildcard *.h) \
-	$(wildcard *.hh) \
-	$(wildcard *.c) \
-	$(wildcard *.cpp) \
-	doc/strip_markdown.pl \
-	Makefile \
-	$(GENERAL_LIST)
-
-BIN_PKG_LIST = $(GENERAL_LIST)
-
-.PHONY: all allall both both-debug install
-
-all: $(HISAT2_BIN_LIST)
-
-allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
-
-both: hisat2-align-s hisat2-align-l hisat2-build-s hisat2-build-l
-
-both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug
-
-DEFS=-fno-strict-aliasing \
-     -DHISAT2_VERSION="\"`cat VERSION`\"" \
-     -DBUILD_HOST="\"`hostname`\"" \
-     -DBUILD_TIME="\"`date`\"" \
-     -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
-     $(FILE_FLAGS) \
-     $(PREF_DEF) \
-     $(MM_DEF) \
-     $(SHMEM_DEF)
-
-#
-# hisat-bp targets
-#
-
-hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
-	$(LIBS) $(SEARCH_LIBS)
-
-hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(DEBUG_FLAGS) \
-	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
-	$(LIBS) $(SEARCH_LIBS)
-
-
-#
-# hisat2-build targets
-#
-
-hisat2-build-s: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
-	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -DMASSIVE_DATA_RLCSA \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
-
-hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
-	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
-
-hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
-	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DMASSIVE_DATA_RLCSA \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
-
-hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
-	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
-	$(INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
-
-#
-# hisat2 targets
-#
-
-hisat2-align-s: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) \
-	$(INC) $(SEARCH_INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
-
-hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \
-	$(INC) $(SEARCH_INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
-
-hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(DEBUG_FLAGS) \
-	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) $(SRA_DEF) -DBOWTIE2 \
-	$(INC) $(SEARCH_INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
-
-hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
-	$(CXX) $(DEBUG_FLAGS) \
-	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \
-	$(INC) $(SEARCH_INC) \
-	-o $@ $< \
-	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
-
-#
-# hisat2-inspect targets
-#
-
-hisat2-inspect-s: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
-	$(CXX) $(RELEASE_FLAGS) \
-	$(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
-	$(INC) -I . \
-	-o $@ $< \
-	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
-
-hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
-	$(CXX) $(RELEASE_FLAGS) \
-	$(RELEASE_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
-	$(INC) -I . \
-	-o $@ $< \
-	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
-
-hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
-	$(CXX) $(DEBUG_FLAGS) \
-	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
-	$(INC) -I . \
-	-o $@ $< \
-	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
-
-hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
-	$(CXX) $(DEBUG_FLAGS) \
-	$(DEBUG_DEFS) $(EXTRA_FLAGS) \
-	$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \
-	$(INC) -I . \
-	-o $@ $< \
-	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
-
-%.o: %.cpp
-	$(CXX) -c $(RELEASE_FLAGS) \
-		$(RELEASE_DEFS) $(EXTRA_FLAGS) \
-		$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \
-		$(INC) -I . $< -o $@ $<
-
-hisat2: ;
-
-hisat2.bat:
-	echo "@echo off" > hisat2.bat
-	echo "perl %~dp0/hisat2 %*" >> hisat2.bat
-
-hisat2-build.bat:
-	echo "@echo off" > hisat2-build.bat
-	echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat
-
-hisat2-inspect.bat:
-	echo "@echo off" > hisat2-inspect.bat
-	echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat
-
-
-.PHONY: hisat2-src
-hisat2-src: $(SRC_PKG_LIST)
-	chmod a+x scripts/*.sh scripts/*.pl
-	mkdir .src.tmp
-	mkdir .src.tmp/hisat2-$(VERSION)
-	zip tmp.zip $(SRC_PKG_LIST)
-	mv tmp.zip .src.tmp/hisat2-$(VERSION)
-	cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-	cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
-	cp .src.tmp/hisat2-$(VERSION)-source.zip .
-	rm -rf .src.tmp
-
-.PHONY: hisat2-bin
-hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
-	chmod a+x scripts/*.sh scripts/*.pl
-	rm -rf .bin.tmp
-	mkdir .bin.tmp
-	mkdir .bin.tmp/hisat2-$(VERSION)
-	if [ -f hisat2.exe ] ; then \
-		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
-	else \
-		zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
-	fi
-	mv tmp.zip .bin.tmp/hisat2-$(VERSION)
-	cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-	cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
-	cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
-	rm -rf .bin.tmp
-
-.PHONY: doc
-doc: doc/manual.inc.html MANUAL
-
-doc/manual.inc.html: MANUAL.markdown
-	pandoc -T "HISAT2 Manual" -o $@ \
-	 --from markdown --to HTML --toc $^
-	perl -i -ne \
-	 '$$w=0 if m|^</body>|;print if $$w;$$w=1 if m|^<body>|;' $@
-
-MANUAL: MANUAL.markdown
-	perl doc/strip_markdown.pl < $^ > $@
-
-# Install per filesystem hierarchy standard:
-# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
-
-.PHONY: install
-install:
-	mkdir -p ${DESTDIR}${PREFIX}/bin
-	${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
-	${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
-		${DESTDIR}${PREFIX}/bin
-
-	mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
-	${INSTALL} -c scripts/*.sh scripts/*.pl *.py \
-		hisatgenotype_modules/hisat*.py \
-		hisatgenotype_scripts/*.py hisatgenotype_scripts/*.sh \
-		${DESTDIR}${PREFIX}/libexec/hisat2
-
-.PHONY: clean
-clean:
-	rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
-	$(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) \
-	hisat2-src.zip hisat2-bin.zip
-	rm -f core.* .tmp.head
-	rm -rf *.dSYM
-
-.PHONY: push-doc
-push-doc: doc/manual.inc.html
-	scp doc/*.*html doc/indexes.txt salz-dmz:/ccb/salz7-data/www/ccb.jhu.edu/html/software/hisat2/
diff --git a/hisat2/patches/patch-Makefile b/hisat2/patches/patch-Makefile
new file mode 100644
index 0000000000..b3e62f2180
--- /dev/null
+++ b/hisat2/patches/patch-Makefile
@@ -0,0 +1,84 @@
+$NetBSD$
+
+# Respect env
+
+--- Makefile.orig	2020-07-24 20:07:54 UTC
++++ Makefile
+@@ -23,9 +23,11 @@
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+-CXX = $(CPP)
++CC	?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
++CPP	?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CXX	?= $(CPP)
++INSTALL	?= install
++
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 0
+@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+ 	MACOS = 1
+ endif
+ 
+-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
++EXTRA_FLAGS += -std=c++11
+ INC += -I. -I third_party 
+ 
+ MM_DEF = 
+@@ -152,31 +154,9 @@ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS)
+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
+ VERSION = $(shell cat VERSION)
+ 
+-# Convert BITS=?? to a -m flag
+-BITS=32
+-ifeq (x86_64,$(shell uname -m))
+-BITS=64
+-endif
+-# msys will always be 32 bit so look at the cpu arch instead.
+-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+-	ifeq (1,$(MINGW))
+-		BITS=64
+-	endif
+-endif
+-BITS_FLAG =
+-
+-ifeq (32,$(BITS))
+-	BITS_FLAG = -m32
+-endif
+-
+-ifeq (64,$(BITS))
+-	BITS_FLAG = -m64
+-endif
+-SSE_FLAG=-msse2
+-
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  = $(CXXFLAGS)
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+@@ -553,6 +533,20 @@ doc/manual.inc.html: MANUAL.markdown
+ 
+ MANUAL: MANUAL.markdown
+ 	perl doc/strip_markdown.pl < $^ > $@
++
++# Install per filesystem hierarchy standard:
++# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
++
++.PHONY: install
++install:
++	mkdir -p ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
++		${DESTDIR}${PREFIX}/bin
++
++	mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
++	${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
++		${DESTDIR}${PREFIX}/libexec/hisat2
+ 
+ .PHONY: clean
+ clean:
diff --git a/hisat2/patches/patch-aligner__sw.h b/hisat2/patches/patch-aligner__sw.h
new file mode 100644
index 0000000000..7e1d534db6
--- /dev/null
+++ b/hisat2/patches/patch-aligner__sw.h
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Support non-x86
+
+--- aligner_sw.h.orig	2020-07-24 20:07:54.000000000 +0000
++++ aligner_sw.h
+@@ -66,11 +66,14 @@
+ 
+ #define INLINE_CUPS
+ 
++#define	SIMDE_ENABLE_NATIVE_ALIASES
++
++// #include <simde/x86/sse2.h>
+ #include <stdint.h>
+ #include <iostream>
+ #include <limits>
+ #include "threading.h"
+-#include <emmintrin.h>
++#include <emmintrin.h>		// Replace this with simde when possible
+ #include "aligner_sw_common.h"
+ #include "aligner_sw_nuc.h"
+ #include "ds.h"
diff --git a/hisat2/patches/patch-hisat2 b/hisat2/patches/patch-hisat2
index 2b70c3c625..ea0ed8175d 100644
--- a/hisat2/patches/patch-hisat2
+++ b/hisat2/patches/patch-hisat2
@@ -1,6 +1,6 @@
 $NetBSD$
 
-# Limit Windows-specific patches to Windows
+# Support BSD, etc.
 
 --- hisat2.orig	2018-11-07 21:43:32 UTC
 +++ hisat2
diff --git a/hisat2/patches/patch-processor__support.h b/hisat2/patches/patch-processor__support.h
new file mode 100644
index 0000000000..b882729882
--- /dev/null
+++ b/hisat2/patches/patch-processor__support.h
@@ -0,0 +1,25 @@
+$NetBSD$
+
+# Support non-x86
+
+--- processor_support.h.orig	2020-07-24 20:07:54 UTC
++++ processor_support.h
+@@ -12,7 +12,7 @@
+ 
+ #if defined(__INTEL_COMPILER)
+ #   define USING_INTEL_COMPILER
+-#elif defined(__GNUC__)
++#elif defined(__GNUC__) && (defined(__amd64__) || defined(__i386__))
+ #   define USING_GCC_COMPILER
+ #   include <cpuid.h>
+ #elif defined(_MSC_VER)
+@@ -52,8 +52,7 @@ class ProcessorSupport { (public)
+ #elif defined(USING_GCC_COMPILER)
+         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
+ #else
+-        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
+-        assert(0);
++	return false;
+ #endif
+         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
+     }
diff --git a/hisat2/patches/patch-sse__util.h b/hisat2/patches/patch-sse__util.h
new file mode 100644
index 0000000000..94df3199bb
--- /dev/null
+++ b/hisat2/patches/patch-sse__util.h
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Support non-x86
+
+--- sse_util.h.orig	2020-07-24 20:07:54.000000000 +0000
++++ sse_util.h
+@@ -20,11 +20,14 @@
+ #ifndef SSE_UTIL_H_
+ #define SSE_UTIL_H_
+ 
++#define SIMDE_ENABLE_NATIVE_ALIASES
++//#include <simde/x86/sse2.h>
++
+ #include "assert_helpers.h"
+ #include "ds.h"
+ #include "limit.h"
+ #include <iostream>
+-#include <emmintrin.h>
++#include <emmintrin.h>		// Replace with simde when possible
+ 
+ class EList_m128i {
+ public:
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