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Old 02-20-2013, 02:13 AM   #1
Location: Spain

Join Date: Aug 2012
Posts: 22
Default Tabix index at contig, start and end??

Hi there,

I have indexed a tab separated file using tabix. In order to do so, I gave tabix the indexes of the columns for the contig, the start position and the end position (let's call these the start index and the end index).

Now, I try to fetch data from my file using the tabix index, so I gave the fetch command a contig, a start and an end position (let's call this the start query and end query). The result is that tabix returns all entries for that contig with an start position between the start and the end queries, but with an end position unbounded.

OK, these results makes sense to me. But, what is the end index for? If the end is unbounded, only the start index should be needed.
Is there any tabix functionality that I'm missing??

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Old 02-20-2013, 03:55 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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From memory, tabix will return any entries within or overlapping the region given by the start-end co-ordinates.
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Old 02-20-2013, 05:23 AM   #3
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Yes that's it I hadn't realized it gave you the partial overlaps .
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