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locks; strict;
comment	@# @;


1.2
date	2021.02.08.01.49.25;	author bacon;	state Exp;
branches;
next	1.1;
commitid	LeuJXahXgOf3BQGC;

1.1
date	2021.01.22.17.07.50;	author bacon;	state Exp;
branches;
next	;
commitid	p2JteL9RJEs1fKEC;


desc
@@


1.2
log
@biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
@
text
@$NetBSD$

# Respect pkgsrc env

--- src/utils/htslib/Makefile.orig	2021-01-23 19:33:26.000000000 +0000
+++ src/utils/htslib/Makefile
@@@@ -22,7 +22,7 @@@@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
+CC     ?= gcc
 AR     = ar
 RANLIB = ranlib
 
@@@@ -33,7 +33,7 @@@@ CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS   = -g -Wall -O2
+CFLAGS   ?= -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
 LDFLAGS  =
 LIBS     = $(htslib_default_libs)
@


1.1
log
@biology/bedtools: import bedtools-2.29.2

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
@
text
@d5 1
a5 1
--- src/utils/htslib/Makefile.orig	2021-01-21 22:49:18.823750624 +0000
@