head	1.1;
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	pkgsrc-2026Q1:1.1.0.10
	pkgsrc-2026Q1-base:1.1
	pkgsrc-2025Q4:1.1.0.8
	pkgsrc-2025Q4-base:1.1
	pkgsrc-2025Q3:1.1.0.6
	pkgsrc-2025Q3-base:1.1
	pkgsrc-2025Q2:1.1.0.4
	pkgsrc-2025Q2-base:1.1
	pkgsrc-2025Q1:1.1.0.2
	pkgsrc-2025Q1-base:1.1;
locks; strict;
comment	@# @;


1.1
date	2025.01.20.17.29.59;	author bacon;	state Exp;
branches;
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commitid	Tl3I5DnOJsXzsfGF;


desc
@@


1.1
log
@biology/subread: Alignment, quantification, SNPs

The Subread package comprises a suite of software programs for
processing next-gen sequencing read data including:

    Subread: a general-purpose read aligner which can align both
    genomic DNA-seq and RNA-seq reads. It can also be used to
    discover genomic mutations including short indels and structural
    variants.

    Subjunc: a read aligner developed for aligning RNA-seq reads
    and for the detection of exon-exon junctions. Gene fusion events
    can be detected as well.

    featureCounts: a software program developed for counting
    reads to genomic features such as genes, exons, promoters and
    genomic bins.

    Sublong: a long-read aligner that is designed based on
    seed-and-vote.

    exactSNP: a SNP caller that discovers SNPs by testing signals
    against local background noises.
@
text
@$NetBSD$

# Respect env

--- longread-one/Makefile.orig	2024-07-25 00:35:55 UTC
+++ longread-one/Makefile
@@@@ -1,12 +1,12 @@@@
-CC_EXEC = gcc
 OPT_LEVEL = 3
 
 include ../makefile.version
 include make.version
 
-CCFLAGS =  ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
-LDFLAGS =  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
-CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb
+CC ?= gcc
+CCFLAGS += -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 \
+	    -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
+LDFLAGS +=  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
 
 ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
 ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
@@@@ -19,9 +19,8 @@@@ clean:
 clean:
 	rm -f *.o LRM
 
-LRM: longread-mapping.c  ${ALL_OBJECTS} 
-	${CC} -o LRM longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
+LRM: longread-mapping.c  ${ALL_OBJECTS}
+	${CC} -o LRM ${CFLAGS} longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
 
 $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
-	$(CC) -o $@@ -c $(subst .o,.c,$@@)
-	
+	$(CC) -o $@@ -c ${CFLAGS} $(subst .o,.c,$@@)
@