Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Major
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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:None
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Story Points:5
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Epic Link:
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Sprint:Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul
Description
When loading a bai file, if no bam file or its header is found, compare the bin sizes of the bai file to the chromosome lengths for the selected genome. Use this comparison to determine the order of the chromosomes. For example if the bin sizes are 16kbp, 32kbp, 64kbp and the chromosome sizes are Chr1:15kbp, Chr2:61kbp, and Chr3:32kbp, the order of the bai file must be Chr1, Chr3, Chr2. Use this to correctly order the chromosomes in the bai graph in IGB.
I put an additional bam and bai in the index hacking google drive:
https://drive.google.com/open?id=1Y9krI6VX3vBzTKEcneGy1McnMJEK739m
human_2009_inOrder_evenNumberChromosomesAndXHaveLessData.bam
This file is from the smoketesting dataset for the 2009 human genome. I went through and chopped out some amount of data on every even numbered chromosome and the X chromosome. I kept the order of the chromosomes as they appear below. Note that the chromosomes are for the most part in order from largest to smallest. However, chr20, chr22, and chrX are out of order in terms of their size.
Order and sizes of chromosomes in bam/bai file
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrM LN:16571
@SQ SN:chrX LN:155270560