BED GRAPH files support #13
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@SilinPavel , thanks! Regarding
Once these issues are fixed, @mzueva and @vpolyakov88 could you please check this feature? |
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@vpolyakov88 here are BedGraph and BIG WIG files that was created from: This files contain information about coverage on a chr3. So you can check that values are the same. For example for me it looks like: full chromosome view: 100 bp view: |
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@SilinPavel , great! |
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@SilinPavel I've found a bug. In case when user zooms to scale 211bp and less in region where end of one region in the same time start of next region (first should be more) second region isn't displaying on attached data go to chr3: 62121 - 62361. |
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@vpolyakov88 Thank you a lot! There was the bug because of losing the last bedGraph feature in a query iterator. It was fixed in 3ddca48. Please check it one more time. And don't hesitate to report me about bugs if any! |
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@SilinPavel New code and refactoring are quite good. Please fix year in the license header and check that all new classes has javadoc. I think that we should refactor hierarchy of AbstactWigManager and FacadeWigManager and use the approach from VcfManager and AbstractVcfReader (do not use autowired beans for stateless file readers). |
docs/md/cli/command-reference.md
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| @@ -222,7 +222,7 @@ ngb reg_file|rf [<REFERENCE_NAME>|<REFERENCE_ID>] [<PATH_TO_NGS_FILE>] [options] | |||
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| Registers a specified file. At least two arguments have to be specified: | |||
| Previously registered reference sequence file from NGB server. Reference file can be addressed by name or an identifier | |||
| Flesystem path foor the file to be registered. BAM, VCF, GFF, GTF, BED, SEG files are accepted. GZipped files are also accepted in a format <FILE_NAME>.<FILE_EXT>.gz, e.g.: my_variants.vcf.gz. | |||
| Flesystem path foor the file to be registered. BAM, VCF, GFF, GTF, BED, SEG, WIG, BED GRAPH files are accepted. GZipped files are also accepted in a format <FILE_NAME>.<FILE_EXT>.gz, e.g.: my_variants.vcf.gz. | |||
| /* | ||
| * MIT License | ||
| * | ||
| * Copyright (c) 2016 EPAM Systems |
| import java.util.stream.Collectors; | ||
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| import static com.epam.catgenome.component.MessageHelper.getMessage; | ||
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| /** | ||
| * Manages all work with BedGraph files. | ||
| * */ | ||
| @Service |
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I think we don't need AbstractWigManager implementations as Spring beans. Task a look at VcfReader interface and it's implementations.
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@mzueva Thanks for the review. Could you clarify some points? Am I right if I think that you propose to autowire all beans that we need into FacadeWigManager and provide it to our AbstractWigManager implementations into their constructors? in this case all AbstractWigManager hierarchy won't be spring beans and will be created simply with constructors call?
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@mzueva take a look one more time please! Now it is more pretty, but bear in mind that we still need to provide the fileManager and the biologicalDataItemManager to a AbstractWigProcessor realization due to we need register and get index into a BedGraphProcessor object. |
Description
Background
The bedGraph format is very popular format, but unfortunately currently NGB does not allow to visualize such files directly, only bigWig files are supported. This pull request directs to add the support of Bed graph files.
Changes
New classes for work with Bed graph files were added. WigManager was split to two classes for a decomposition and also BedGraph manager was invented as a child to AbstractWigManager.
FacadeWigManager currently get calls from WigController and delegate it to right implementation of AbstractWigManager.
Acceptance criteria
All tests must pass and also manually registration, viewing of BigWig and BedGraph files should be performed.
Check list