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List data access patterns in Picard/GATK/Foghorn #1

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akiezun opened this issue Dec 10, 2014 · 4 comments
Closed

List data access patterns in Picard/GATK/Foghorn #1

akiezun opened this issue Dec 10, 2014 · 4 comments
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@akiezun
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akiezun commented Dec 10, 2014

We need to understand the data access patterns in the existing engines: Picard/GATK/Foghorn
@lbergelson and @kshakir already started doing it. Can you move the list here?
@akiezun
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akiezun commented Dec 11, 2014

The doc is here -it may be easier to edit as a google doc. https://docs.google.com/a/broadinstitute.org/document/d/10j9UvZQ_jOY2vKz59eHrRdrazxHUscs1DnWan5sVTao/edit#

@nh13
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nh13 commented Dec 11, 2014

Can someone here take inventory of the various Picard tools that you want to consider moving over? These are NOT represented in the GATK best practices document, for example MergeBamAlignment or ValidateSamFile.

@akiezun
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akiezun commented Dec 12, 2014

@nh13 my sense is that most of picard tools (non-private ones) will either be moved over to hellbender or we'll keep linking to picard (but the latter seems suboptimal - there should be just one toolkit)

@akiezun akiezun added this to the Aye-aye milestone Dec 15, 2014
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akiezun commented Jan 9, 2015

this is done

@akiezun akiezun closed this as completed Jan 9, 2015
@droazen droazen mentioned this issue Jun 18, 2015
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@cmnbroad cmnbroad mentioned this issue Dec 8, 2015
Open
@cmnbroad cmnbroad mentioned this issue Oct 22, 2018
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@davidbenjamin davidbenjamin mentioned this issue Mar 13, 2019
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ldgauthier added a commit that referenced this issue Aug 2, 2019
@ldgauthier
Item #1 -- remove instanceof call and let every GATKTool have default
c41b05d 
GenomicsDB options
ldgauthier added a commit that referenced this issue Aug 5, 2019
@ldgauthier
Item #1 -- remove instanceof call and let every GATKTool have default
2f65547 
GenomicsDB options
@AlijahArcher AlijahArcher mentioned this issue Feb 1, 2021
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@LN908 LN908 mentioned this issue May 19, 2021
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@rsasch rsasch mentioned this issue May 26, 2021
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lucidtronix added a commit that referenced this issue Jul 27, 2021
@lucidtronix
Move ML4CVD over (#1)
94735af 
add ml4cvd files
@jdjdj0202 jdjdj0202 mentioned this issue May 29, 2023
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mcovarr added a commit that referenced this issue Aug 8, 2023
@mcovarr
empty commit #1
e2c8096
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@kshakir @nh13 @akiezun