/usr/share/doc/python-pysam/tests/Makefile is in python-pysam-tests 0.7.7-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | all: ex1.pileup.gz ex1.bam.bai \
ex2.sam.gz ex2.sam ex1.sam \
ex2.bam \
ex3.bam ex3.bam.bai \
ex4.bam ex4.bam.bai \
ex5.bam ex5.bam.bai \
ex6.bam \
ex8.bam ex8.bam.bai \
ex9_nofail.bam.bai \
ex9_fail.bam.bai \
ex10.bam ex10.bam.bai \
example_unmapped_reads_no_sq.bam \
example_user_header.bam \
example_btag.bam \
example_bai.bam \
softclip.bam
ex2.sam.gz: ex1.bam ex1.bam.bai
samtools view -h ex1.bam | gzip > ex2.sam.gz
%.bam: %.sam ex1.fa.fai
samtools import ex1.fa.fai $< $@
%.sam: %.sam.gz
gunzip < $< > $@
ex1.fa.fai:ex1.fa
samtools faidx ex1.fa
ex1.bam:ex1.sam.gz ex1.fa.fai
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
%.bam.bai:%.bam
samtools index $<
ex1.pileup.gz:ex1.bam ex1.fa
samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
touch tmp.list
samtools import tmp.list $< $@
rm -f tmp.list
example_bai.bam: ex1.bam
cp ex1.bam $@
samtools index $@
mv $@.bai example_bai.bai
softclip.bam: softclip.sam
samtools view -bS $< > $@
clean:
mkdir keep_bam_files
mv ex9_fail.bam ex9_nofail.bam example_btag.bam example_empty_header.bam issue100.bam tag_bug.bam test_unaligned.bam keep_bam_files
rm -fr *.bam *.bai *.fai *.pileup* \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam
mv keep_bam_files/* .
rmdir keep_bam_files
rm -rf pysam_test_work/
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