Details
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Type: New Feature
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Status: Closed (View Workflow)
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Priority: Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2.5
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Epic Link:
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Sprint:Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep
Description
The track operation Depth Graph (All) is used to summarize the depth of reads. It does not include soft-clipped parts of the read.
Add Depth Graph (Soft-clip) as a track operation for bam/sam. This would create a depth graph for just soft-clip parts of reads.
This should be possible to do by copying how Depth Graph (All) functions, but using only syms of instance BamSoftChildSingletonSeqSym.
Attachments
Issue Links
Activity
Please see my current progress and notes regarding this issue:
https://bitbucket.org/pbadzuh/igb_pbdev/branch/IGBF-1443#diff
- The changes I have made create a new track operation UI element and configure it for use in the code.
- The new operation can be seen by opening a bam file in IGB (requires that a respective bai file be present in the same directory), right-clicking on the BAM track title (on the left) -> Track Operations -> Depth Graph (Soft-clip All).
- Todo: Update the collectSoftclipSpans method in the getSymmetrySoftclipSummary method (SoftClipDepthOperator.java) such that only the spans of soft-clip portions of aligned reads are extracted.
- Step through the collectStartSpans and collectLeafSpans methods using the netbeans debugger to understand the data structures and methods being used. This is where I stopped; the output of these methods seemed to be the same with the test files I used, however, this doesn’t seem to be correct. I was not able to identify what exactly constitutes a ‘start span’, so that my be a good start.
- The getSpanSummary function called afterward in getSymmetrySoftclipSummary should generate a depth graph for the entire portions of the isolated soft-clip spans of aligned reads. Should be kept as is.
- I have attached the files I used for testing. Additional files that may be useful in testing can be found here.
Philip Badzuh (Inactive)
added a comment - Please see my current progress and notes regarding this issue:
https://bitbucket.org/pbadzuh/igb_pbdev/branch/IGBF-1443#diff
The changes I have made create a new track operation UI element and configure it for use in the code.
The new operation can be seen by opening a bam file in IGB (requires that a respective bai file be present in the same directory), right-clicking on the BAM track title (on the left) -> Track Operations -> Depth Graph (Soft-clip All).
Todo: Update the collectSoftclipSpans method in the getSymmetrySoftclipSummary method ( SoftClipDepthOperator.java ) such that only the spans of soft-clip portions of aligned reads are extracted.
Step through the collectStartSpans and collectLeafSpans methods using the netbeans debugger to understand the data structures and methods being used. This is where I stopped; the output of these methods seemed to be the same with the test files I used, however, this doesn’t seem to be correct. I was not able to identify what exactly constitutes a ‘start span’, so that my be a good start.
The getSpanSummary function called afterward in getSymmetrySoftclipSummary should generate a depth graph for the entire portions of the isolated soft-clip spans of aligned reads. Should be kept as is.
I have attached the files I used for testing. Additional files that may be useful in testing can be found here .
Tested master dmg installer for Mac.
Depth Graph (Soft-clip All) working correctly.
Closing issue.