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