head	1.1;
access;
symbols
	pkgsrc-2026Q1:1.1.0.22
	pkgsrc-2026Q1-base:1.1
	pkgsrc-2025Q4:1.1.0.20
	pkgsrc-2025Q4-base:1.1
	pkgsrc-2025Q3:1.1.0.18
	pkgsrc-2025Q3-base:1.1
	pkgsrc-2025Q2:1.1.0.16
	pkgsrc-2025Q2-base:1.1
	pkgsrc-2025Q1:1.1.0.14
	pkgsrc-2025Q1-base:1.1
	pkgsrc-2024Q4:1.1.0.12
	pkgsrc-2024Q4-base:1.1
	pkgsrc-2024Q3:1.1.0.10
	pkgsrc-2024Q3-base:1.1
	pkgsrc-2024Q2:1.1.0.8
	pkgsrc-2024Q2-base:1.1
	pkgsrc-2024Q1:1.1.0.6
	pkgsrc-2024Q1-base:1.1
	pkgsrc-2023Q4:1.1.0.4
	pkgsrc-2023Q4-base:1.1
	pkgsrc-2023Q3:1.1.0.2
	pkgsrc-2023Q3-base:1.1;
locks; strict;
comment	@# @;


1.1
date	2023.08.12.14.58.35;	author bacon;	state Exp;
branches;
next	;
commitid	CaJleqsQNe31zvAE;


desc
@@


1.1
log
@biology/stringtie: RNA-Seq assembly and quantification

StringTie is a fast and highly efficient assembler of RNA-seq alignments
into potential transcripts. The input can be the alignments of raw reads
as usual; it also accepts longer assembled sequences. The output can be
processed by downstream software including Ballgown, Cuffdiff, etc.
@
text
@$NetBSD$

# Respect CC, CFLAGS

--- samtools-0.1.18/Makefile.orig	2018-03-06 16:29:49 UTC
+++ samtools-0.1.18/Makefile
@@@@ -1,5 +1,5 @@@@
-CC=			gcc
-CFLAGS=		-g -Wall -fsigned-char -O2 #-m64 #-arch ppc
+CC?=			gcc
+CFLAGS?=		-g -Wall -fsigned-char -O2 #-m64 #-arch ppc
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 #-D_USE_KNETFILE 
 KNETFILE_O=	knetfile.o
 LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
@