Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb
Description
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: Within the BAI index visualization handler plugin, write code to identify if there is a readable bam file. The bam file should be located in the same directory as the bai file and should have the same name as the bai file, but with a .bam extension. Note that the bai itself may have .bam in front of the .bai extension (EXAMPLE.bam.bai). If a bam file is present, use the appropriate Samtools method to retrieve the bam header.
Able to read bam file header.
Closing issue.