Document SAMRecord flag-setting about readthedocs HOT 3 CLOSED

I restored it with this commit but did not add it to the TOC. @melissachang do you want to make any changes to it before I push it to live?

http://google-genomics.readthedocs.org/en/staging/migrating_tips.html

from readthedocs.

I don't think we should restore
http://google-genomics.readthedocs.org/en/staging/migrating_tips.html since
v1beta doesn't exist anymore.

It seems like the flags pseudocode in migrating_tips.html is useful, even
though we don't have v1beta anymore. Maybe add a section to
http://google-genomics.readthedocs.org/en/staging/use_cases/run_picard_and_gatk/index.html?highlight=picard
?

Whereever you end up putting it, please also update the url in
https://github.com/googlegenomics/gatk-tools-java/blob/e0375190427bb44057691b4461c0a91f0761e6d8/src/main/java/com/google/cloud/genomics/gatk/common/GenomicsConverter.java#L158

On Tue, May 12, 2015 at 5:26 PM Nicole Deflaux [email protected]
wrote:

I restored it with this commit
af1ae7a
but did not add it to the TOC. @melissachang
https://github.com/melissachang do you want to make any changes to it
before I push it to live?

http://google-genomics.readthedocs.org/en/staging/migrating_tips.html

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#36 (comment)
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from readthedocs.

Okay, I will proceed with restoring it (its unlinked so it won't be too much clutter) and I added issue https://github.com/googlegenomics/gatk-tools-java/issues/15 for the real fix. Thanks @melissachang !

from readthedocs.