type twobit = ([ `twobit ], [ `binary ]) Bistro.Std.fileclass type chrom_sizes = object ... endtype bigBed = ([ `bigBed ], [ `binary ]) Bistro.Std.fileclass type bedGraph = object ... endtype wig = ([ `wig ], [ `text ]) Bistro.Std.filetype bigWig = ([ `bigWig ], [ `binary ]) Bistro.Std.fileval string_of_genome : [< genome ] -> stringval chromosome_sequence :
[< genome ] ->
string ->
Defs.fasta Bistro.Std.workflowDealing with genome sequences
val chromosome_sequences :
[< genome ] ->
[ `ucsc_chromosome_sequences ] Bistro.Std.directory Bistro.Std.workflowval genome_sequence : [< genome ] -> Defs.fasta Bistro.Std.workflowval genome_2bit_sequence : [< genome ] -> twobit Bistro.Std.workflowval twoBitToFa :
Defs.bed4 Bistro.Std.workflow ->
twobit Bistro.Std.workflow ->
Defs.fasta Bistro.Std.workflowval fetchChromSizes : [< genome ] -> chrom_sizes Bistro.Std.workflowChromosome size and clipping
val bedClip :
chrom_sizes Bistro.Std.workflow ->
Defs.bed3 as 'a Bistro.Std.workflow ->
'a Bistro.Std.workflowval bedGraphToBigWig :
[< genome ] ->
bedGraph Bistro.Std.workflow ->
bigWig Bistro.Std.workflowConversion between annotation file formats
val bedToBigBed :
[< genome ] ->
[ `bed3 of Defs.bed3 Bistro.Std.workflow
| `bed5 of Defs.bed5 Bistro.Std.workflow ] ->
bigBed Bistro.Std.workflowbedToBigBed
utility. Fails when given an empty BED file on input.
val bedToBigBed_failsafe :
[< genome ] ->
[ `bed3 of Defs.bed3 Bistro.Std.workflow
| `bed5 of Defs.bed5 Bistro.Std.workflow ] ->
bigBed Bistro.Std.workflowsam as Ucsc_gb.bedToBigBed but produces an empty file when given an empty BED on input.