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BoutrosLaboratory / bamql

Query language for filtering SAM/BAM reads
http://labs.oicr.on.ca/boutros-lab/software/BAMQL
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Filtering by read start positions #18

Closed zxl124 closed 4 years ago

zxl124 commented 4 years ago

Hi, is it possible to filter reads based on the start position? The current options "after()", "before()", and "position()" does not work for this purpose because they filter reads covering the positions. What I want is filtering reads starting at a certain position. I see in your manual that "begin" would return the start position of reads. I've tried "chr(1) & begin==1000", "chr(1) & begin(1000)", "chr(1) & begin : 1000", and none of these works. I guess I just don't know how your query language work. Could you give some guidance on how to do that? Thank you.

zxl124 commented 4 years ago

Oh, sorry, never mind. I see I am missing spaces between "begin" and the position.