bistro 0.3.0 · OCaml Package

type 'a output

val bigwig : Ucsc_gb.bigWig output

val bedgraph : Ucsc_gb.bedGraph output

val bamcoverage : 
  ?scalefactor:float ->
  ?filterrnastrand:[ `forward | `reverse ] ->
  ?binsize:int ->
  ?blacklistfilename:[ `bed | `gtf ] Bistro.Std.workflow ->
  ?threads:int ->
  ?normalizeto1x:int ->
  ?normalizeusingrpkm:bool ->
  ?ignorefornormalization:string list ->
  ?skipnoncoveredregions:bool ->
  ?smoothlength:int ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  'a output ->
  [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ->
  'a Bistro.Std.workflow

val bamcompare : 
  ?scalefactormethod:[ `readcount | `ses ] ->
  ?samplelength:int ->
  ?numberofsamples:int ->
  ?scalefactor:string ->
  ?ratio:
    [ `log2
    | `ratio
    | `subtract
    | `add
    | `mean
    | `reciprocal_ratio
    | `first
    | `second ] ->
  ?pseudocount:int ->
  ?binsize:int ->
  ?region:string ->
  ?blacklistfilename:[ `bed | `gtf ] Bistro.Std.workflow ->
  ?threads:int ->
  ?normalizeto1x:int ->
  ?normalizeusingrpkm:bool ->
  ?ignorefornormalization:string list ->
  ?skipnoncoveredregions:bool ->
  ?smoothlength:int ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  'a output ->
  [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ->
  [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ->
  'a Bistro.Std.workflow

val bigwigcompare : 
  ?scalefactor:string ->
  ?ratio:
    [ `log2
    | `ratio
    | `subtract
    | `add
    | `mean
    | `reciprocal_ratio
    | `first
    | `second ] ->
  ?pseudocount:int ->
  ?binsize:int ->
  ?region:string ->
  ?blacklistfilename:[ `bed | `gtf ] Bistro.Std.workflow ->
  ?threads:int ->
  'a output ->
  [ `bigwig ] Bistro.Std.workflow ->
  [ `bigwig ] Bistro.Std.workflow ->
  'a Bistro.Std.workflow

class type compressed_numpy_array = object ... end

val multibamsummary_bins : 
  ?binsize:int ->
  ?distancebetweenbins:int ->
  ?region:string ->
  ?blacklistfilename:[ `bed | `gtf ] Bistro.Std.workflow ->
  ?threads:int ->
  ?outrawcounts:bool ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  Defs.indexed_bam Bistro.Std.workflow list ->
  compressed_numpy_array Bistro.Std.workflow

val multibamsummary_bed : 
  ?region:string ->
  ?blacklistfilename:[ `bed | `gtf ] Bistro.Std.workflow ->
  ?threads:int ->
  ?outrawcounts:bool ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  ?metagene:bool ->
  ?transcriptid:bool ->
  ?exonid:bool ->
  ?transcriptiddesignator:bool ->
  Defs.bed3 Bistro.Std.workflow ->
  Defs.indexed_bam Bistro.Std.workflow list ->
  compressed_numpy_array Bistro.Std.workflow

package bistro