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subread: High-performance read alignment, quantification, mutation discovery
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Tue Mar 30 11:16:48 2021 -0500
Changeset: 04d4d27de5b024f40e21c255126bada215c6345e
Modified Files:
Makefile
Added Files:
subread/DESCR
subread/Makefile
subread/PLIST
subread/distinfo
subread/files/Makefile.pkg
subread/patches/patch-HelperFunctions.c
subread/patches/patch-core-junction.c
subread/patches/patch-gene-algorithms.c
subread/patches/patch-input-files.c
subread/patches/patch-long-hashtable.c
subread/patches/patch-longread-one_LRMsorted-hashtable.c
subread/patches/patch-longread-one_Makefile
subread/patches/patch-longread-one_longread-mapping.c
subread/patches/patch-read-repair.c
subread/patches/patch-sambam-file.c
subread/patches/patch-sorted-hashtable.c
subread/patches/patch-subread.h
Log Message:
subread: High-performance read alignment, quantification, mutation discovery
Begin port from FreeBSD
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=04d4d27de5b024f40e21c255126bada215c6345e
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
subread/DESCR | 13 +++
subread/Makefile | 33 +++++++
subread/PLIST | 1 +
subread/distinfo | 18 ++++
subread/files/Makefile.pkg | 104 +++++++++++++++++++++
subread/patches/patch-HelperFunctions.c | 22 +++++
subread/patches/patch-core-junction.c | 12 +++
subread/patches/patch-gene-algorithms.c | 22 +++++
subread/patches/patch-input-files.c | 13 +++
subread/patches/patch-long-hashtable.c | 13 +++
.../patch-longread-one_LRMsorted-hashtable.c | 17 ++++
subread/patches/patch-longread-one_Makefile | 32 +++++++
.../patches/patch-longread-one_longread-mapping.c | 40 ++++++++
subread/patches/patch-read-repair.c | 12 +++
subread/patches/patch-sambam-file.c | 15 +++
subread/patches/patch-sorted-hashtable.c | 17 ++++
subread/patches/patch-subread.h | 13 +++
18 files changed, 398 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index b091788410..086d4a4189 100644
--- a/Makefile
+++ b/Makefile
@@ -5267,6 +5267,7 @@ SUBDIR+= stress-ng
SUBDIR+= strongswan
SUBDIR+= structure
SUBDIR+= stumpwm
+SUBDIR+= subread
SUBDIR+= suitesparse
SUBDIR+= sulley
SUBDIR+= sunterlib
diff --git a/subread/DESCR b/subread/DESCR
new file mode 100644
index 0000000000..dffe014722
--- /dev/null
+++ b/subread/DESCR
@@ -0,0 +1,13 @@
+The Subread package comprises a suite of software programs for processing
+next-gen sequencing read data including:
+ Subread: a general-purpose read aligner which can align both genomic
+ DNA-seq and RNA-seq reads. It can also be used to discover genomic
+ mutations including short indels and structural variants.
+ Subjunc: a read aligner developed for aligning RNA-seq reads and for the
+ detection of exon-exon junctions. Gene fusion events can be detected as
+ well.
+ featureCounts: a software program developed for counting reads to genomic
+ features such as genes, exons, promoters and genomic bins.
+ Sublong: a long-read aligner that is designed based on seed-and-vote.
+ exactSNP: a SNP caller that discovers SNPs by testing signals against local
+ background noises.
diff --git a/subread/Makefile b/subread/Makefile
new file mode 100644
index 0000000000..25a07c28af
--- /dev/null
+++ b/subread/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Tue Mar 30 11:06:45 CDT 2021 #
+###########################################################
+
+# LIB_DEPENDS= libsysinfo.so:devel/libsysinfo
+
+DISTNAME= subread-2.0.2-source
+PKGNAME= subread-2.0.2
+CATEGORIES= biology
+# FreeBSD MASTER_SITES: SF/${PORTNAME}/${PORTNAME}-${PV}
+MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=subread/}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://bioinf.wehi.edu.au/subread-package/
+COMMENT= High-performance read alignment, quantification and mutation discovery
+LICENSE= gnu-gpl-v3
+
+USE_TOOLS+= gmake
+
+WRKSRC= ${WRKDIR}/subread-2.0.2-source/src
+
+CFLAGS+= -fcommon
+MAKE_FILE= ${FILESDIR}/Makefile.pkg
+INSTALL_TARGET= install-strip
+
+# Convert any _DEPENDS above that have a buildlink3.mk
+# .include "../..///buildlink3.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/subread/PLIST b/subread/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/subread/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/subread/distinfo b/subread/distinfo
new file mode 100644
index 0000000000..2304991298
--- /dev/null
+++ b/subread/distinfo
@@ -0,0 +1,18 @@
+$NetBSD$
+
+SHA1 (subread-2.0.2-source.tar.gz) = 1f5eb1ffa0184e21321fb9e40a9f02dd94bb19ff
+RMD160 (subread-2.0.2-source.tar.gz) = 2cfa127a7bea963d67330edee2ca226f9d6dde49
+SHA512 (subread-2.0.2-source.tar.gz) = 549164aadcd1e05cd1f941a4c10d6e19f904d2d75dae8391bbf3003a26e13f6a14cc22618662c2baf804b4d020a58e7ba0b0be9b4ff1181ad981a24270ffb64e
+Size (subread-2.0.2-source.tar.gz) = 23295764 bytes
+SHA1 (patch-HelperFunctions.c) = b1205dfe8c57a9033237086e39ffa8e362595bf2
+SHA1 (patch-core-junction.c) = 39b7acbc4a61c40c112c8451ab234bb06d189462
+SHA1 (patch-gene-algorithms.c) = e8f4f0e5747cba279bf8fb88a0743a58065cf7a4
+SHA1 (patch-input-files.c) = cd85b2df930eba3f910c534d93933bf4f4355cd3
+SHA1 (patch-long-hashtable.c) = c6d6fef3c6925e94d7267db23dcba97aa5ad71a3
+SHA1 (patch-longread-one_LRMsorted-hashtable.c) = 956bc03d1ce3e820a61b81bd2d524916a33e0bce
+SHA1 (patch-longread-one_Makefile) = aae55c436af25e5513e79f4dcd6aee03d2dc48d2
+SHA1 (patch-longread-one_longread-mapping.c) = 9179704c5fc3dda691e8d13e08bb5dbe66f93e44
+SHA1 (patch-read-repair.c) = 848fd626695cbe494b2579d7f18d6b5381986811
+SHA1 (patch-sambam-file.c) = 6c6edfbefcffece7c5e296e8224884f6ac34445d
+SHA1 (patch-sorted-hashtable.c) = 68cbf2b4cc516d825ccdd4260d7b2a38e9e4dd3c
+SHA1 (patch-subread.h) = f259b8dfd4d3394f4dbeee5ab5c3ac4f6bb76308
diff --git a/subread/files/Makefile.pkg b/subread/files/Makefile.pkg
new file mode 100644
index 0000000000..2ae783e699
--- /dev/null
+++ b/subread/files/Makefile.pkg
@@ -0,0 +1,104 @@
+
+
+include makefile.version
+
+CCFLAGS = -DMAKE_FOR_EXON -DMAKE_STANDALONE \
+ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64
+LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm
+CC ?= gcc
+CC += ${CCFLAGS}
+
+BINS = detectionCall sublong repair txUnique featureCounts removeDup \
+ exactSNP subread-buildindex subindel subread-align subjunc \
+ qualityScores subread-fullscan propmapped flattenGTF \
+
+MKDIR ?= mkdir -p
+INSTALL ?= install
+DESTDIR ?= .
+PREFIX ?= local
+STRIP ?= strip
+
+ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
+ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
+ALL_H=$(addsuffix .h, ${ALL_LIBS})
+ALL_C=$(addsuffix .c, ${ALL_LIBS})
+
+all: genRandomReads detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped flattenGTF # samMappedBases mergeVCF testZlib
+ mkdir -p ../bin/utilities
+ mv longread-one/LRM longread-one/sublong
+ mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
+ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
+
+sublong: longread-one/longread-mapping.c ${ALL_OBJECTS}
+ echo " " > longread-one/make.version
+ rm -f longread-one/*.o
+ cd longread-one && $(MAKE)
+
+genRandomReads: gen_rand_reads.c ${ALL_OBJECTS}
+ ${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
+
+flattenGTF: flattenAnnotations.c ${ALL_OBJECTS}
+ ${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
+
+detectionCall: detection-calls.c ${ALL_OBJECTS}
+ ${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
+
+repair: read-repair.c ${ALL_OBJECTS}
+ ${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
+
+txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS}
+ ${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
+
+globalReassembly: global-reassembly.c ${ALL_OBJECTS}
+ ${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
+
+propmapped: propmapped.c ${ALL_OBJECTS}
+ ${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
+
+exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS}
+ ${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS}
+ ${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
+
+removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS}
+ ${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS}
+ ${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
+
+featureCounts: readSummary.c subread.h ${ALL_OBJECTS}
+ ${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subread-align: core-interface-aligner.c ${ALL_OBJECTS}
+ ${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subjunc: core-interface-subjunc.c ${ALL_OBJECTS}
+ ${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subtools: subtools.c ${ALL_OBJECTS}
+ ${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
+
+qualityScores: qualityScores.c ${ALL_OBJECTS}
+ ${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
+
+subread-fullscan: fullscan.c ${ALL_OBJECTS}
+ ${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
+
+.PHONY: clean install install-strip
+
+install-strip: install
+ ${STRIP} ${DESTDIR}${PREFIX}/bin/*
+
+install:
+ ${MKDIR} ${DESTDIR}${PREFIX}/bin
+ ${INSTALL} -c \
+ ../bin/exactSNP \
+ ../bin/featureCounts \
+ ../bin/sub* \
+ ../bin/utilities/* \
+ ${DESTDIR}${PREFIX}/bin
+
+clean:
+ rm -f core featureCounts exactSNP removeDup subread-buildindex \
+ ${ALL_OBJECTS}
diff --git a/subread/patches/patch-HelperFunctions.c b/subread/patches/patch-HelperFunctions.c
new file mode 100644
index 0000000000..201347784d
--- /dev/null
+++ b/subread/patches/patch-HelperFunctions.c
@@ -0,0 +1,22 @@
+$NetBSD$
+
+--- HelperFunctions.c.orig 2020-06-04 23:58:40 UTC
++++ HelperFunctions.c
+@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2)
+
+ int mac_str(char * str_buff)
+ {
+-#if defined(FREEBSD) || defined(__MINGW32__)
++#if defined(__FreeBSD__) || defined(__MINGW32__)
+ return 1;
+ #else
+ #ifdef MACOS
+@@ -2703,7 +2703,7 @@ void main(){
+
+ int get_free_total_mem(size_t * total, size_t * free_mem){
+
+-#ifdef FREEBSD
++#ifdef __FreeBSD__
+ return -1;
+ #endif
+
diff --git a/subread/patches/patch-core-junction.c b/subread/patches/patch-core-junction.c
new file mode 100644
index 0000000000..fef3248934
--- /dev/null
+++ b/subread/patches/patch-core-junction.c
@@ -0,0 +1,12 @@
+$NetBSD$
+
+--- core-junction.c.orig 2018-11-08 15:19:02 UTC
++++ core-junction.c
+@@ -22,6 +22,7 @@
+ #include <string.h>
+ #include <ctype.h>
+ #include <assert.h>
++#include <unistd.h>
+ #include "subread.h"
+ #include "sublog.h"
+ #include "gene-value-index.h"
diff --git a/subread/patches/patch-gene-algorithms.c b/subread/patches/patch-gene-algorithms.c
new file mode 100644
index 0000000000..10d02f179d
--- /dev/null
+++ b/subread/patches/patch-gene-algorithms.c
@@ -0,0 +1,22 @@
+$NetBSD$
+
+--- gene-algorithms.c.orig 2021-03-30 13:51:05 UTC
++++ gene-algorithms.c
+@@ -29,7 +29,7 @@
+ #include <sys/stat.h>
+ #include <sys/types.h>
+
+-#ifndef FREEBSD
++#ifndef __FreeBSD__
+ #include <sys/timeb.h>
+ #endif
+
+@@ -1568,7 +1568,7 @@ int load_offsets(gene_offset_t* offsets , const char i
+
+ double miltime(){
+ double ret;
+- #ifdef FREEBSD
++ #ifdef __FreeBSD__
+ struct timeval tp;
+ struct timezone tz;
+ tz.tz_minuteswest=0;
diff --git a/subread/patches/patch-input-files.c b/subread/patches/patch-input-files.c
new file mode 100644
index 0000000000..823b842c13
--- /dev/null
+++ b/subread/patches/patch-input-files.c
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- input-files.c.orig 2020-06-05 00:33:03 UTC
++++ input-files.c
+@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo
+ #ifdef __MINGW32__
+ return fopen64(fname, mode);
+ #else
+-#if defined(__LP64__) || defined(_LP64) || defined(MACOS)
++#if defined(__LP64__) || defined(_LP64) || defined(MACOS) || defined(__FreeBSD__)
+ return fopen(fname, mode);
+ #else
+ return fopen64(fname, mode);
diff --git a/subread/patches/patch-long-hashtable.c b/subread/patches/patch-long-hashtable.c
new file mode 100644
index 0000000000..9139fa87e1
--- /dev/null
+++ b/subread/patches/patch-long-hashtable.c
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- long-hashtable.c.orig 2020-06-04 23:59:33 UTC
++++ long-hashtable.c
+@@ -22,7 +22,7 @@
+ #include <string.h>
+
+ #ifndef MACOS
+-#ifndef FREEBSD
++#ifndef __FreeBSD__
+ #include <malloc.h>
+ #endif
+ #endif
diff --git a/subread/patches/patch-longread-one_LRMsorted-hashtable.c b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
new file mode 100644
index 0000000000..ecce900e7c
--- /dev/null
+++ b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
@@ -0,0 +1,17 @@
+$NetBSD$
+
+--- longread-one/LRMsorted-hashtable.c.orig 2018-11-08 14:47:43 UTC
++++ longread-one/LRMsorted-hashtable.c
+@@ -22,11 +22,9 @@
+ #include <string.h>
+ #include "LRMsorted-hashtable.h"
+
+-#ifndef MACOS
+-#ifndef FREEBSD
++#if !defined(__APPLE__) && !defined(__FreeBSD__)
+ #include <malloc.h>
+ #endif
+-#endif
+
+ #include<math.h>
+ #include "LRMfile-io.h"
diff --git a/subread/patches/patch-longread-one_Makefile b/subread/patches/patch-longread-one_Makefile
new file mode 100644
index 0000000000..7feb65ace2
--- /dev/null
+++ b/subread/patches/patch-longread-one_Makefile
@@ -0,0 +1,32 @@
+$NetBSD$
+
+--- longread-one/Makefile.orig 2019-09-04 04:22:49 UTC
++++ longread-one/Makefile
+@@ -1,12 +1,12 @@
+-CC_EXEC = gcc
+ OPT_LEVEL = 3
+
+ include ../makefile.version
+ include make.version
+
+-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
+-LDFLAGS = -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+-CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb
++CC ?= gcc
++CFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \
++ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
++LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+
+ ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
+ ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
+@@ -20,8 +20,8 @@ clean:
+ rm -f *.o LRM
+
+ LRM: longread-mapping.c ${ALL_OBJECTS}
+- ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
++ ${CC} -o LRM ${CFLAGS} longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
+
+ $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
+- $(CC) -o $@ -c $(subst .o,.c,$@)
++ $(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@)
+
diff --git a/subread/patches/patch-longread-one_longread-mapping.c b/subread/patches/patch-longread-one_longread-mapping.c
new file mode 100644
index 0000000000..40d4b6c740
--- /dev/null
+++ b/subread/patches/patch-longread-one_longread-mapping.c
@@ -0,0 +1,40 @@
+$NetBSD$
+
+--- longread-one/longread-mapping.c.orig 2021-03-30 13:58:29 UTC
++++ longread-one/longread-mapping.c
+@@ -30,7 +30,9 @@
+ #ifndef __MINGW32__
+ #include <sys/resource.h>
+ #endif
++#ifndef __FreeBSD__
+ #include <sys/timeb.h>
++#endif
+ #include <sys/stat.h>
+ #include <locale.h>
+ #include <ctype.h>
+@@ -225,6 +227,17 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte
+ #endif
+ double LRMmiltime(){
+ double ret;
++#ifdef __FreeBSD__
++
++ struct timeval tp;
++ struct timezone tz;
++ tz.tz_minuteswest=0;
++ tz.tz_dsttime=0;
++ gettimeofday(&tp,&tz);
++ ret = tp.tv_sec+ 0.001*0.001* tp.tv_usec;
++
++#else
++
+ #ifdef LRM_CLOCK_USE_GETTIME
+ struct timespec tsc;
+ clock_gettime(CLOCK_REALTIME, &tsc);
+@@ -235,6 +248,7 @@ double LRMmiltime(){
+ ret = trp.time*1.0+(trp.millitm*1.0/1000.0);
+ #endif
+
++#endif
+ return ret;
+ }
+
diff --git a/subread/patches/patch-read-repair.c b/subread/patches/patch-read-repair.c
new file mode 100644
index 0000000000..77210ad03b
--- /dev/null
+++ b/subread/patches/patch-read-repair.c
@@ -0,0 +1,12 @@
+$NetBSD$
+
+--- read-repair.c.orig 2018-11-08 15:20:06 UTC
++++ read-repair.c
+@@ -3,6 +3,7 @@
+ #include <string.h>
+ #include <getopt.h>
+ #include <zlib.h>
++#include <unistd.h>
+ #include "subread.h"
+ #include "core.h"
+ #include "input-files.h"
diff --git a/subread/patches/patch-sambam-file.c b/subread/patches/patch-sambam-file.c
new file mode 100644
index 0000000000..b53a634b58
--- /dev/null
+++ b/subread/patches/patch-sambam-file.c
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- sambam-file.c.orig 2018-11-08 15:20:35 UTC
+--- sambam-file.c.orig 2021-03-27 07:38:08.000000000 +0000
++++ sambam-file.c
+@@ -30,6 +30,7 @@
+ #include <string.h>
+ #include <assert.h>
+ #include <ctype.h>
++#include <unistd.h>
+ #include "subread.h"
+ #include "core.h"
+ #include "HelperFunctions.h"
diff --git a/subread/patches/patch-sorted-hashtable.c b/subread/patches/patch-sorted-hashtable.c
new file mode 100644
index 0000000000..104dc22335
--- /dev/null
+++ b/subread/patches/patch-sorted-hashtable.c
@@ -0,0 +1,17 @@
+$NetBSD$
+
+--- sorted-hashtable.c.orig 2018-11-08 03:33:50 UTC
++++ sorted-hashtable.c
+@@ -23,11 +23,9 @@
+ #include <stdlib.h>
+ #include <string.h>
+
+-#ifndef MACOS
+-#ifndef FREEBSD
++#if !defined(__FreeBSD__) && !defined(__APPLE__)
+ #include <malloc.h>
+ #endif
+-#endif
+
+ #include<math.h>
+ #include"core.h"
diff --git a/subread/patches/patch-subread.h b/subread/patches/patch-subread.h
new file mode 100644
index 0000000000..40f91694a8
--- /dev/null
+++ b/subread/patches/patch-subread.h
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- subread.h.orig 2018-11-08 14:46:06 UTC
++++ subread.h
+@@ -102,7 +102,7 @@
+
+ #define USE_POSIX_MUTEX_LOCK
+
+-#if defined(MACOS) || defined(FREEBSD) || defined(USE_POSIX_MUTEX_LOCK)
++#if defined(__APPLE__) || defined(__FreeBSD__) || defined(USE_POSIX_MUTEX_LOCK)
+ typedef pthread_mutex_t subread_lock_t;
+ #define pthread_spinlock_t pthread_mutex_t
+ #define pthread_spin_lock pthread_mutex_lock
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