mykola/freebsd-ports
1
0
Fork 0
forked from Lainports/freebsd-ports
Code Pull requests Activity

biology/sam2pairwise: Show pairwise alignment for each read in a SAM file

Browse source 
sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
reconstruct the pairwise alignment of each read.
This commit is contained in:
Jason W. Bacon 2021-09-07 15:32:29 -05:00
parent ff638362c3
commit e61df5e464
5 changed files with 67 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
biology/Makefile
View file

@ -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

20
biology/sam2pairwise/Makefile Normal file
View file

@ -0,0 +1,20 @@
PORTNAME= sam2pairwise
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.0
CATEGORIES= biology
MAINTAINER= jwb@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>

3
biology/sam2pairwise/distinfo Normal file
View file

@ -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

39
biology/sam2pairwise/files/patch-Makefile Normal file
View file

@ -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

4
biology/sam2pairwise/pkg-descr Normal file
View file

@ -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