Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / debian / patches / no-pileup-tests.patch

diff --git a/debian/patches/no-pileup-tests.patch b/debian/patches/no-pileup-tests.patch
new file mode 100644 (file)
index 0000000..26532ab
--- /dev/null
+++ b/debian/patches/no-pileup-tests.patch
@@ -0,0 +1,22 @@
+--- a/examples/Makefile
++++ b/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
++      ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.bcf calDepth
+               @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
+ 
+ ex1.fa.fai:ex1.fa
+@@ -8,12 +8,6 @@
+               ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+ ex1.bam.bai:ex1.bam
+               ../samtools index ex1.bam
+-ex1.pileup.gz:ex1.bam ex1.fa
+-              ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+-ex1.glf:ex1.bam ex1.fa
+-              ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+-ex1.glfview.gz:ex1.glf
+-              ../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+ 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