git: 2e559ca48c93 - main - biology/bfc: Correct sequencing errors from Illumina sequencing data

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=2e559ca48c93b075905245367e11e30b9be34b2c

commit 2e559ca48c93b075905245367e11e30b9be34b2c
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-23 17:28:41 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-08-23 17:28:41 +0000

    biology/bfc: Correct sequencing errors from Illumina sequencing data
    
    BFC is a standalone high-performance tool for correcting sequencing
    errors from Illumina sequencing data. It is specifically designed for
    high-coverage whole-genome human data, though also performs well for
    small genomes.
---
 biology/Makefile                  |  1 +
 biology/bfc/Makefile              | 20 ++++++++++++++++++++
 biology/bfc/distinfo              |  3 +++
 biology/bfc/files/patch-Makefile  | 36 ++++++++++++++++++++++++++++++++++++
 biology/bfc/files/patch-kthread.c | 10 ++++++++++
 biology/bfc/pkg-descr             |  6 ++++++
 6 files changed, 76 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 24a2bc0890c3..b3a5731f8a6a 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -9,6 +9,7 @@
     SUBDIR += bbmap
     SUBDIR += bcftools
     SUBDIR += bedtools
+    SUBDIR += bfc
     SUBDIR += bioawk
     SUBDIR += biococoa
     SUBDIR += biolibc
diff --git a/biology/bfc/Makefile b/biology/bfc/Makefile
new file mode 100644
index 000000000000..967e8829f16a
--- /dev/null
+++ b/biology/bfc/Makefile
@@ -0,0 +1,20 @@
+PORTNAME=	bfc
+DISTVERSION=	g20150417
+CATEGORIES=	biology
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Correct sequencing errors from Illumina sequencing data
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+USES=		gmake
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	lh3
+GH_TAGNAME=	69ab176e
+
+INSTALL_TARGET=	install-strip
+PLIST_FILES=	bin/bfc bin/hash2cnt
+
+.include <bsd.port.mk>
diff --git a/biology/bfc/distinfo b/biology/bfc/distinfo
new file mode 100644
index 000000000000..b2e518d4e0c8
--- /dev/null
+++ b/biology/bfc/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1629673065
+SHA256 (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 202913e590421d23571c5e7c5cb9c23730ee57cb5b2eaa0e7806d33c49482452
+SIZE (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 68138
diff --git a/biology/bfc/files/patch-Makefile b/biology/bfc/files/patch-Makefile
new file mode 100644
index 000000000000..b031139aa596
--- /dev/null
+++ b/biology/bfc/files/patch-Makefile
@@ -0,0 +1,36 @@
+--- Makefile.orig	2015-04-17 05:17:58 UTC
++++ Makefile
+@@ -1,11 +1,17 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
++CC?=		gcc
++# Allow env to set optimization and warning levels, then add required flags
++CFLAGS?=	-g -Wall -O2
++CFLAGS+=	-Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
+ CPPFLAGS=
+ INCLUDES=	
+ OBJS=		kthread.o utils.o bseq.o bbf.o htab.o count.o correct.o bfc.o
+ PROG=		bfc hash2cnt
+ LIBS=		-lm -lz -lpthread
+ 
++MKDIR?=		mkdir
++INSTALL?=	install
++STRIP?=		strip
++
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+@@ -18,6 +24,13 @@ bfc:$(OBJS)
+ 
+ hash2cnt:hash2cnt.o
+ 		$(CC) $(CFLAGS) $< -o $@
++
++install:
++		$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++		$(INSTALL) -c $(PROG) $(DESTDIR)$(PREFIX)/bin
++
++install-strip: install
++		$(STRIP) $(DESTDIR)$(PREFIX)/bin/*
+ 
+ clean:
+ 		rm -fr gmon.out *.o ext/*.o a.out $(PROG) *~ *.a *.dSYM session*
diff --git a/biology/bfc/files/patch-kthread.c b/biology/bfc/files/patch-kthread.c
new file mode 100644
index 000000000000..a019b17beea5
--- /dev/null
+++ b/biology/bfc/files/patch-kthread.c
@@ -0,0 +1,10 @@
+--- kthread.c.orig	2021-08-22 22:59:48 UTC
++++ kthread.c
+@@ -1,6 +1,7 @@
+ #include <pthread.h>
+ #include <stdlib.h>
+ #include <limits.h>
++#include <inttypes.h>
+ 
+ /************
+  * kt_for() *
diff --git a/biology/bfc/pkg-descr b/biology/bfc/pkg-descr
new file mode 100644
index 000000000000..a2135b6a4ecc
--- /dev/null
+++ b/biology/bfc/pkg-descr
@@ -0,0 +1,6 @@
+BFC is a standalone high-performance tool for correcting sequencing
+errors from Illumina sequencing data. It is specifically designed for
+high-coverage whole-genome human data, though also performs well for
+small genomes.
+
+WWW: https://github.com/lh3/bfc