Is it possible to specify track url and indexURL as query parameters?

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Dmitriy Sonkin

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May 15, 2019, 3:58:03 PM5/15/19
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Is it possible to specify track url and corresponding track indexURL to BAM file as query parameters?
If it's possible it would be great if working example can be provided.
Below is URL with query parameters based on example in documentation, however it does not specify index and does not load BAM file.

James Robinson

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May 15, 2019, 4:21:22 PM5/15/19
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Its possible that BAM file has been deleted.  Im traveling now, and am limited in what I can do on a phone, but the parameter should be “index” or “indexURL”


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James Robinson

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May 16, 2019, 9:07:26 AM5/16/19
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Hi,
Apologies, I examined the code and it does not support an index parameter currently.   I've put that on my list for the next release.  If your bam file index follows standard naming convention you do not need to specfiy the index,  try the following URL.    

Dmitriy Sonkin

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May 16, 2019, 12:00:53 PM5/16/19
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Thank you for follow up and providing working example. Unfortunately in number of cases bam file index name follows standard naming convention, but unique file identifiers are different resulting in different URLs. Below is example of URLs which should be useful for testing of index parameter.

gs://gdc-ccle-open/98a0206b-29f5-42d3-957b-6480e2fde185/G20483.HCC-15.2.bam
gs://gdc-ccle-open/78c0b917-0e41-4faa-a96c-3550b8377d78/G20483.HCC-15.2.bam.bai

On Thursday, May 16, 2019 at 9:07:26 AM UTC-4, James Robinson wrote:
Hi,
Apologies, I examined the code and it does not support an index parameter currently.   I've put that on my list for the next release.  If your bam file index follows standard naming convention you do not need to specfiy the index,  try the following URL.    

On Wed, May 15, 2019 at 4:21 PM James Robinson <jrob...@broadinstitute.org> wrote:
Its possible that BAM file has been deleted.  Im traveling now, and am limited in what I can do on a phone, but the parameter should be “index” or “indexURL”

On Wed, May 15, 2019 at 3:58 PM Dmitriy Sonkin <dms...@gmail.com> wrote:
Is it possible to specify track url and corresponding track indexURL to BAM file as query parameters?
If it's possible it would be great if working example can be provided.
Below is URL with query parameters based on example in documentation, however it does not specify index and does not load BAM file.

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