Details

    • Story Points:
      2
    • Sprint:
      Fall 2018 1, Fall 2018 Sprint 2

      Description

      Support newer VCF formats in IGB.

      (User request)

        Attachments

        1. Diffs4.1To4.2
          7 kB
          Ivory Blakley
        2. Diffs4.2To4.3
          126 kB
          Ivory Blakley

          Issue Links

            Activity

            Hide
            ieclabau Ivory Blakley (Inactive) added a comment - - edited

            I think it will be best to talk through the code comments in person. Sneha and I can talk through this on Tuesday afternoon.

            Notes from in-person review:
            remove the code that was commented out in core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
            line 328

            core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
            line 520

            Otherwise, comments were addressed in discussion. No need for further testing. Remove the commented code and create pull request.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - - edited I think it will be best to talk through the code comments in person. Sneha and I can talk through this on Tuesday afternoon. Notes from in-person review: remove the code that was commented out in core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java line 328 core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java line 520 Otherwise, comments were addressed in discussion. No need for further testing. Remove the commented code and create pull request.
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            I made those changes, rebased onto upstream master, and created a pull request.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - I made those changes, rebased onto upstream master, and created a pull request.
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            ann.loraine commented on pull request #623: IGBF-1380 Support VCF4.2

            How is this more efficient? Does it reduce:

            • processing time (less work per line of data)
            • memory usage (how much?)
              It seems to me that the main value of this change is it reduces complexity of the code, making it easier to understand and maintain.

            _________________

            You are right. "more efficient" was not the right phrase. "simpler" is better.
            I reduced the comments that I added for the INFO and FORMAT sub-class definitions in VCF.java.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - ann.loraine commented on pull request #623: IGBF-1380 Support VCF4.2 How is this more efficient? Does it reduce: processing time (less work per line of data) memory usage (how much?) It seems to me that the main value of this change is it reduces complexity of the code, making it easier to understand and maintain. _________________ You are right. "more efficient" was not the right phrase. "simpler" is better. I reduced the comments that I added for the INFO and FORMAT sub-class definitions in VCF.java.
            Hide
            ann.loraine Ann Loraine added a comment -

            Merged into master

            Show
            ann.loraine Ann Loraine added a comment - Merged into master
            Hide
            mason Mason Meyer (Inactive) added a comment -

            My testing verifies that all VCF versions are now compatible with IGB and load as expected. There was no exception noted in the console during my testing and all other file formats are loading as expected, so this story will now be closed.

            Show
            mason Mason Meyer (Inactive) added a comment - My testing verifies that all VCF versions are now compatible with IGB and load as expected. There was no exception noted in the console during my testing and all other file formats are loading as expected, so this story will now be closed.

              People

              • Assignee:
                stiwari8 Srishti Tiwari (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: