1 Description: disable samtools pileup commands in the example tests.
2 ‘samtools pileup’ has been dropped in version 0.1.17.
3 Forwarded: samtools-devel@lists.sourceforge.net
6 --- a/examples/Makefile
7 +++ b/examples/Makefile
9 all:../libbam.a ../samtools ../bcftools/bcftools \
10 - ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
11 + ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.bcf calDepth
12 @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
16 ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
18 ../samtools index ex1.bam
19 -ex1.pileup.gz:ex1.bam ex1.fa
20 - ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
21 -ex1.glf:ex1.bam ex1.fa
22 - ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
23 -ex1.glfview.gz:ex1.glf
24 - ../samtools glfview ex1.glf | gzip > ex1.glfview.gz
26 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@