1 all: ex1.pileup.gz ex1.bam.bai \
2 ex2.sam.gz ex2.sam ex1.sam \
11 ex10.bam ex10.bam.bai \
12 example_unmapped_reads_no_sq.bam \
13 example_user_header.bam \
16 ex2.sam.gz: ex1.bam ex1.bam.bai
17 samtools view -h ex1.bam | gzip > ex2.sam.gz
19 %.bam: %.sam ex1.fa.fai
20 samtools import ex1.fa.fai $< $@
27 ex1.bam:ex1.sam.gz ex1.fa.fai
28 samtools import ex1.fa.fai ex1.sam.gz ex1.bam
31 ex1.pileup.gz:ex1.bam ex1.fa
32 samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
34 example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
36 samtools import tmp.list $< $@
40 rm -fr *.bam *.bai *.fai *.pileup* \
41 *~ calDepth *.dSYM pysam_*.sam \
42 ex2.sam ex2.sam.gz ex1.sam