/usr/share/elk/anfo.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.
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; ELK extension for Anfo
;
; Loads the Anfo library and provides a wrappers/ convenience functions.
; TODO: decide whether output streams should return anything.
; bind missing "calculating" streams.
; take the returning of results out of the C code (mostly...)
(require 'srfi-89)
(load "/usr/lib/x86_64-linux-gnu/libanfo.la")
(define *default-compression* 99)
(define *default-handles-limit* 128)
(define *default-mem-limit* 512)
(define *default-origin* 33)
(define *default-solexa-scale* #f)
; sets sensible verbosity, but also makes sure that libanfo was actually loaded
(set-verbosity! 'warning)
; invokes continuation on stream, extracts a result, frees the stream
; The stream is always freed, even on non-local exit. The result is
; only extracted in the normal control flow.
(define (bracket-stream stream)
(lambda (cont)
(dynamic-wind
(lambda () #f)
(lambda () (let ((rs (cont stream))
(r0 (get-summary stream)))
(if r0 (cons r0 rs) rs)))
(lambda () (prim-delete-stream stream)))))
(define chop: 'chop:)
(define compress: 'compress:)
(define context: 'context:)
(define editor: 'editor:)
(define genome: 'genome:)
(define genomes: 'genomes:)
(define handles: 'handles:)
(define intercept: 'intercept:)
(define label: 'label:)
(define left: 'left:)
(define max: 'max:)
(define mem: 'mem:)
(define min: 'min:)
(define name: 'name:)
(define num: 'num:)
(define origin: 'origin:)
(define primary: 'primary:)
(define prior: 'prior:)
(define quality: 'quality:)
(define right: 'right:)
(define score: 'score:)
(define secondary: 'secondary:)
(define sequences: 'sequences:)
(define slope: 'slope:)
(define solexa: 'solexa:)
(define strict: 'strict:)
(define (write-fasta file) (bracket-stream (prim-write-fasta file)))
(define (write-fastq file) (bracket-stream (prim-write-fastq file)))
(define (write-glz file) (bracket-stream (prim-write-glz file)))
(define (write-sam file) (bracket-stream (prim-write-sam file)))
(define (write-table file) (bracket-stream (prim-write-table file)))
(define (write-text file) (bracket-stream (prim-write-text file)))
(define (write-threealn file) (bracket-stream (prim-write-threealn file)))
(define (write-wiggle file) (bracket-stream (prim-write-wiggle file)))
(define*
(duct-tape (label: lbl "contig")
(prior: pri 0.0))
(bracket-stream (prim-duct-tape lbl pri)))
(define*
(add-alns (context: ctx 0)
(strict: str #f))
(bracket-stream (prim-add-alns ctx str)))
(define*
(read-file in
(solexa: sol *default-solexa-scale*)
(origin: ori *default-origin*)
(genome: gen "")
(name: nam #f))
(bracket-stream (prim-read-file in sol ori gen nam)))
(define (filter-chain left right file) (bracket-stream (prim-filter-chain left right file)))
(define (filter-qual qual) (bracket-stream (prim-filter-qual qual)))
(define (inside-region file) (bracket-stream (prim-inside-region file)))
(define (mask-qual qual) (bracket-stream (prim-mask-qual qual)))
(define (outside-region file) (bracket-stream (prim-outside-region file)))
(define (sanitize) (bracket-stream (prim-sanitize)))
(define (subsample rate) (bracket-stream (prim-subsample rate)))
(define*
(filter-length (min: min 0)
(max: max #f))
(bracket-stream (prim-filter-length min max)))
(define*
(filter-gc (min: min 0)
(max: max 100))
(bracket-stream (prim-filter-gc min max)))
(define*
(filter-multi (num: num 2))
(bracket-stream (prim-filter-multi num)))
(define*
(edit-header (editor: editor #f))
(bracket-stream (prim-edit-header editor)))
(define*
(filter-score (slope: slope 7.5)
(intercept: intercept 20)
(genomes: genomes '()))
(bracket-stream (prim-filter-score slope intercept genomes)))
(define*
(filter-total-score (slope: slope 7.5)
(intercept: intercept 20)
(genomes: genomes '(hg18 pt2)))
(bracket-stream (prim-filter-total-score slope intercept genomes)))
(define*
(filter-mapq mapq (genomes '()))
(bracket-stream (prim-filter-mapq mapq genomes)))
(define*
(require-best-hit (genomes: g '()) (sequences: s '()))
(bracket-stream (prim-require-bht g s)))
(define*
(require-hit (genomes: g '()) (sequences: s '()))
(bracket-stream (prim-require-hit g s)))
(define*
(ignore-hit (genomes: g '()) (sequences: s '()))
(bracket-stream (prim-ignore-hit g s)))
(define*
(only-genomes (genomes '()))
(bracket-stream (prim-only-genomes genomes)))
(define*
(sort-pos genomes
(mem: m *default-mem-limit*)
(handles: h *default-handles-limit*))
(bracket-stream (prim-sort-pos m h genomes)))
(define*
(sort-name (mem: m *default-mem-limit*)
(handles: h *default-handles-limit*))
(bracket-stream (prim-sort-name m h)))
(define*
(rmdup (slope: slope 7.5)
(intercept: intercept 20)
(quality: qual 40))
(bracket-stream (prim-rmdup slope intercept qual)))
(define*
(trim (left: left '())
(right: right '())
(score: score 4))
(bracket-stream (prim-trim left right score)))
(define (stats)
(let* ((p (lambda (lo hi) (+ lo (* hi 65536 32768))))
(fun (lambda (total mapped mapped_u different
bases_gc_lo bases_gc_hi
bases_gc_m_lo bases_gc_m_hi
bases_lo bases_hi
bases_2_lo bases_2_hi
bases_m_lo bases_m_hi
bases_m2_lo bases_m2_hi)
`(( total . ,total )
( mapped . ,mapped )
( mapuniq . ,mapped_u )
( distinct . ,different )
( gc-raw . ,(* 100 (/ (p bases_gc_lo bases_gc_hi) (p bases_lo bases_hi))))
( gc-mapped . ,(* 100 (/ (p bases_gc_m_lo bases_gc_m_hi) (p bases_m_lo bases_m_hi))))
( bases . ,(p bases_lo bases_hi))
( bases-m2 . ,(p bases_2_lo bases_2_hi))
( mapbases . ,(p bases_m_lo bases_m_hi))
( mapbases-m2 . ,(p bases_m2_lo bases_m2_hi))))))
(fmap (lambda (args) (apply fun args))
(bracket-stream (prim-stats)))))
(define (mismatches) (bracket-stream (prim-mismatches)))
(define (vector-dot v w)
(let loop ((s 0) (l (vector->list v)) (r (vector->list w)))
(if (or (null? l) (null? r))
s
(loop (+ s (* (car l) (car r)))
(cdr l) (cdr r)))))
(define (vector-mul v x)
(apply vector (map (lambda (y) (* y x)) (vector->list v))))
(define (mat-times-vector m v)
(apply vector (map (lambda (w) (vector-dot w v)) (vector->list m))))
(define*
(divergence (primary: p)
(secondary: s)
(chop: c))
(let ((fun
(lambda (b)
(let* ((d1 (vector-dot b '#(3 -1 3 -1 -1)))
(e (/ (* (- (vector-ref b 2)
(vector-ref b 3))
3)
d1))
(d (- (* 4 e)
3))
(a (vector-mul
(mat-times-vector
`#( #( ,(- e 3) 0 ,e 0 0 )
#( 0 ,(- e 3) 0 ,e ,e )
#( ,(* 3 e) 0 ,(- (* 3 e) 3) 0 0 )
#( 0 ,e 0 ,(- e 3) ,e )
#( 0 ,(* 2 e) 0 ,(* 2 e) ,(- (* 2 e) 3) ) )
b)
(/ 1 d))))
`(( error-rate . ,e )
( corrected-div . ,(/ (* 2 (vector-ref a 3)) (+ (vector-ref a 1) (vector-ref a 3))))
( corrected-counts . ,a )
( raw-div . ,(/ (* 2 (vector-ref b 3)) (+ (vector-ref b 1) (vector-ref b 3))))
( raw-counts . ,b ))))))
(fmap fun (bracket-stream (prim-divergence p s c)))))
(define*
(write-file out
(compress: comp *default-compression*))
(bracket-stream (prim-write-native out comp)))
(define write-native write-file)
(define (anfo-with-input in)
(cond
((procedure? in) in)
(else (bracket-stream (prim-read-file in *default-solexa-scale* *default-origin* "" #f)))))
(define (anfo-with-output out)
(cond
((procedure? out) out)
((string? out) (bracket-stream (prim-write-native out *default-compression*)))
(else (error 'anfo-with-output "object does not denote an output stream: ~s" out))))
(define (anfo-with-many-inputs args cont) (anfo-with-many anfo-with-input args cont))
(define (anfo-with-many-outputs args cont) (anfo-with-many anfo-with-output args cont))
(define (anfo-with-many-filters args cont) (anfo-with-many (lambda (x) x) args cont))
(define (anfo-with-many fun args cont)
(if (null? args)
(cont '())
((fun (car args))
(lambda (s)
(anfo-with-many
fun
(cdr args)
(lambda (ss) (cont (cons s ss))))))))
(define (tee . args)
(lambda (cont)
(anfo-with-many-outputs
args
(lambda (outs)
((bracket-stream
(apply prim-tee outs))
cont)))))
(define (chain . args)
(lambda (cont)
(anfo-with-many-filters
args
(lambda (outs)
((bracket-stream
(apply prim-chain outs))
cont)))))
(define (merge . args)
(lambda (cont)
(anfo-with-many-inputs
args
(lambda (outs)
((bracket-stream
(apply prim-merge outs))
cont)))))
(define (join . args)
(lambda (cont)
(anfo-with-many-inputs
args
(lambda (outs)
((bracket-stream
(apply prim-join outs))
cont)))))
(define (concat . args)
(lambda (cont)
(anfo-with-many-inputs
args
(lambda (outs)
((bracket-stream
(apply prim-concat outs))
cont)))))
(define (anfo-run . args)
((anfo-with-input (car args))
(lambda (in-stream)
((anfo-with-output (apply chain (cdr args)))
(lambda (out-stream)
(prim-anfo-run in-stream out-stream))))))
(define (fmap fun stream)
(lambda (cont)
(let ((rs (stream cont)))
(cons (fun (car rs)) (cdr rs)))))
(provide 'anfo)
(autoload 'pp 'pp.scm)
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