Implement Depth Graph (Soft-clip)

Philip Badzuh (Inactive) added a comment - 31/Aug/20 11:06 AM 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 .