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SplitIntervals should give output ".interval_list" suffix #5390

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ldgauthier opened this issue Nov 2, 2018 · 1 comment
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SplitIntervals should give output ".interval_list" suffix #5390

ldgauthier opened this issue Nov 2, 2018 · 1 comment

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@ldgauthier
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SplitIntervals writes a Picard-style interval list with a SAMTextHeader sequence dictionary (i.e. header starting with @), but currently the output file extension is .intervals and Picard won't read in the file unless it has a *.interval_list extension.
lbergelson added a commit that referenced this issue Nov 2, 2018
@lbergelson
ScatterIntervals produces interval_list instead of intervals
8c508a0 
* This matches what picard expects an interval list to be named.
* Added a new --extension argument to allow changing the extension.
* Fixes #5390
@lbergelson lbergelson mentioned this issue Nov 2, 2018
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lbergelson added a commit that referenced this issue Nov 5, 2018
@lbergelson
ScatterIntervals produces interval_list instead of intervals
1ac0038 
* This matches what picard expects an interval list to be named.
* Added a new --extension argument to allow changing the extension.
* Fixes #5390
lbergelson added a commit that referenced this issue Nov 6, 2018
@lbergelson
ScatterIntervals produces interval_list instead of intervals (#5392)
2b48dcf 
* This matches what picard expects an interval list to be named.
* Added a new --extension argument to allow changing the extension .
* Fixes #5390
@ldgauthier
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Thanks @lbergelson !

EdwardDixon pushed a commit to EdwardDixon/gatk that referenced this issue Nov 9, 2018
@lbergelson @EdwardDixon
ScatterIntervals produces interval_list instead of intervals (broadin…
56d443d 
…stitute#5392)

* This matches what picard expects an interval list to be named.
* Added a new --extension argument to allow changing the extension .
* Fixes broadinstitute#5390
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@ldgauthier