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SAM=$(wildcard *.sam)
BAM=$(SAM:%.sam=%.bam)
BAI=$(BAM:%.bam=%.bam.bai)
CRAM=ex1.cram ex2.cram ex3.cram
CRAI=$(CRAM:%.cram=%.cram.crai)
# ex2.bam - bam file without index
all: ex1.pileup.gz \
ex1.sam ex1.bam \
ex2.sam.gz ex2.sam ex2.bam ex2.bam.bai \
uncompressed.bam \
$(BAM) $(BAI) \
$(CRAM) $(CRAI) \
example_bai.bam \
rg_with_tab.bam \
ex2_truncated.bam \
empty.bam empty.bam.bai \
explicit_index.bam explicit_index.cram \
faidx_empty_seq.fq.gz \
ex1.fa.gz ex1.fa.gz.fai \
ex1_csi.bam
# ex2.sam - as ex1.sam, but with header
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 $< $@
uncompressed.bam: ex2.sam
samtools view -buS $< > $@
%.bam: %.sam
samtools view -bS $< > $@
%.cram: %.sam
samtools view -bC -T ex1.fa $< > $@
%.cram.crai: %.cram
samtools index $<
%.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 mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
ex2_truncated.bam: ex2.bam
head -c 124000 ex2.bam > ex2_truncated.bam
ex1_csi.bam: ex1.bam
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
empty.bam: ex2.sam
grep "^@" $< | samtools view -Sb - > $@
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
explicit_index.bam: ex1.bam
cp ex1.bam $@
explicit_index.cram: ex1.cram
cp ex1.cram $@
clean:
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
%.fq.gz: %.fq
gzip < $< > $@
%.fa.gz: %.fa
bgzip < $< > $@
%.fa.gz.fai: %.fa.gz
samtools faidx $<
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