The following commit has been merged in the master branch:
commit 8d8550e9e349d7a3e910bc64a8cbbaeba67112d2
Author: Charles Plessy <[email protected]>
Date: Sat Mar 30 16:42:22 2013 +0900
Pass -lpthread when compiling calDepth.
diff --git a/debian/patches/fix_example_makefile.patch
b/debian/patches/fix_example_makefile.patch
index af42493..d3db4aa 100644
--- a/debian/patches/fix_example_makefile.patch
+++ b/debian/patches/fix_example_makefile.patch
@@ -3,8 +3,10 @@ Description: disable samtools pileup commands in the example
tests.
Forwarded: [email protected]
Origin: vendor
---- a/examples/Makefile
-+++ b/examples/Makefile
+Index: samtools/examples/Makefile
+===================================================================
+--- samtools.orig/examples/Makefile
++++ samtools/examples/Makefile
@@ -1,5 +1,5 @@
all:../libbam.a ../samtools ../bcftools/bcftools \
- ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam
ex1.glfview.gz ex1.bcf calDepth
@@ -25,3 +27,12 @@ Origin: vendor
ex1a.bam:ex1.bam
../samtools view -h ex1.bam | awk
'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view
-bS - > $@
ex1b.bam:ex1.bam
+@@ -40,7 +34,7 @@
+ (cd ..; make libbam.a)
+
+ calDepth:../libbam.a calDepth.c
+- gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz
++ gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz
-lpthread
+
+ clean:
+ rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM
ex1*.rg ex1.bcf
--
Processing of sequence alignments in SAM and BAM formats.
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