/usr/share/doc/anfo/example/threebam.scm is in anfo 0.98-5.
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 | (load 'anfo.scm)
(set-verbosity 'info)
(anfo-run
(chain
(concat "foo.anfo" "bar.anfo")
(filter-score slope: 7.5 intercept: 20))
(chain
(only-genomes "hg18")
require-hit
(write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/hg18.map -o hg18.bam -"))
(chain
(only-genomes "pt2")
require-hit
(write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/pt2.map -o pt2.bam -"))
(chain
(only-genomes "hcscca")
require-hit
(write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/hcscca.map -o hcscca.bam -")))
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