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This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 25 Jun 2015 15:02:35 +0200
Subject: [PATCH] Link with libbam.a if provided via LIBBAM
---
Makefile | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/Makefile b/Makefile
index e334f2f..de310e4 100644
--- a/preseq-master/Makefile
+++ b/preseq-master/Makefile
@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
ifdef SAMTOOLS_DIR
+ifdef LIBBAM
+LIBS += -pthread
+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
+ $(LIBBAM)
+else
bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
$(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
endif
+endif # SAMTOOLS_DIR
+
%.o: %.cpp %.hpp
$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
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