Modernise samtools view option usage
Remove long-unneeded -S "SAM input" option; fix conflicting -bC
"BAM---no, CRAM!---output" options; use -o instead of redirection.
@@ -36,13 +36,13 @@ with_md.sam.gz: ex2.bam ex1.fa
# samtools view $(NO_PG) -bo $@ -t ex1.fa.fai $<
uncompressed.bam: ex2.sam
- samtools view $(NO_PG) -buS $< > $@
+ samtools view $(NO_PG) -bu -o $@ $<
%.bam: %.sam
- samtools view $(NO_PG) -bS $< > $@
+ samtools view $(NO_PG) -bo $@ $<
%.cram: %.sam
- samtools view $(NO_PG) -bC -T ex1.fa $< > $@
+ samtools view $(NO_PG) -Co $@ -T ex1.fa $<
%.cram.crai: %.cram
samtools index $<
@@ -70,7 +70,7 @@ ex1_csi.bam: ex1.bam
samtools index -c ex1_csi.bam
empty.bam: ex2.sam
- grep "^@" $< | samtools view $(NO_PG) -Sb - > $@
+ grep "^@" $< | samtools view $(NO_PG) -bo $@ -
example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
touch tmp.list
