git: e61df5e46475 - main - biology/sam2pairwise: Show pairwise alignment for each read in a SAM file

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e61df5e464758cb1d460c95b4fbb3855a4f7f6dc

commit e61df5e464758cb1d460c95b4fbb3855a4f7f6dc
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-09-07 20:32:29 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-09-07 20:32:29 +0000

    biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
    
    sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
    reconstruct the pairwise alignment of each read.
---
 biology/Makefile                          |  1 +
 biology/sam2pairwise/Makefile             | 20 ++++++++++++++++
 biology/sam2pairwise/distinfo             |  3 +++
 biology/sam2pairwise/files/patch-Makefile | 39 +++++++++++++++++++++++++++++++
 biology/sam2pairwise/pkg-descr            |  4 ++++
 5 files changed, 67 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index f97c311da9fe..294a87ca4e78 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -171,6 +171,7 @@
     SUBDIR += rubygem-bio-executables
     SUBDIR += rubygem-bio-old-biofetch-emulator
     SUBDIR += rubygem-bio-shell
+    SUBDIR += sam2pairwise
     SUBDIR += samtools
     SUBDIR += scrm
     SUBDIR += seaview
diff --git a/biology/sam2pairwise/Makefile b/biology/sam2pairwise/Makefile
new file mode 100644
index 000000000000..dd578353e5a9
--- /dev/null
+++ b/biology/sam2pairwise/Makefile
@@ -0,0 +1,20 @@
+PORTNAME=	sam2pairwise
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.0.0
+CATEGORIES=	biology
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Show pairwise alignment for each read in a SAM file
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKDIR}/${PORTNAME}-${PORTVERSION}/LICENSE
+
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	mlafave
+
+WRKSRC_SUBDIR=	src
+ALL_TARGET=	sam2pairwise
+PLIST_FILES=	bin/sam2pairwise
+
+.include <bsd.port.mk>
diff --git a/biology/sam2pairwise/distinfo b/biology/sam2pairwise/distinfo
new file mode 100644
index 000000000000..364e6c8bde7c
--- /dev/null
+++ b/biology/sam2pairwise/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1631041315
+SHA256 (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 899d3db071cc248870bbedbdb39784de4c54c9a7888bc408022e809ace47ec0e
+SIZE (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 10013
diff --git a/biology/sam2pairwise/files/patch-Makefile b/biology/sam2pairwise/files/patch-Makefile
new file mode 100644
index 000000000000..56ed56b8a857
--- /dev/null
+++ b/biology/sam2pairwise/files/patch-Makefile
@@ -0,0 +1,39 @@
+--- Makefile.orig	2014-08-22 20:02:24 UTC
++++ Makefile
+@@ -1,8 +1,19 @@
+-CXX = g++
+-CC = g++
++CXX	?= g++
++LD	= ${CXX}
+ 
+-sam2pairwise:		sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o translate_cigar.o translate_md.o 
++OBJS	= sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o \
++	translate_cigar.o translate_md.o 
+ 
++PREFIX	?= /usr/local
++DESTDIR	?= .
++INSTALL	?= install
++MKDIR	?= mkdir
++
++all:	sam2pairwise
++
++sam2pairwise:	${OBJS}
++	${CXX} ${OBJS} -o sam2pairwise
++
+ isolate_md.o:		isolate_md.cc isolate_md.hh
+ 
+ shift_cigar.o:		shift_cigar.cc shift_cigar.hh
+@@ -15,6 +26,11 @@ translate_md.o:		translate_md.cc translate_md.hh
+ 
+ sam2pairwise.o:		sam2pairwise.cc isolate_md.hh shift_cigar.hh shift_md.hh translate_cigar.hh translate_md.hh
+ 
+-clobber:
+-	rm -f *.o core sam2pairwise
++.PHONY:	install clean
+ 
++install:
++	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c sam2pairwise ${DESTDIR}${PREFIX}/bin
++
++clean:
++	rm -f *.o core sam2pairwise
diff --git a/biology/sam2pairwise/pkg-descr b/biology/sam2pairwise/pkg-descr
new file mode 100644
index 000000000000..800de1d7998e
--- /dev/null
+++ b/biology/sam2pairwise/pkg-descr
@@ -0,0 +1,4 @@
+sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
+reconstruct the pairwise alignment of each read.
+
+WWW: https://github.com/mlafave/sam2pairwise