Added read-likelihoods array base structure to substitute existing Map-of-Map-of-Maps.

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Valentin Ruano-Rubio 2014-08-12 18:04:43 -04:00

parent 242cd0e58f

commit 4f993e8dbe

8 changed files with 331 additions and 302 deletions

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java

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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java

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public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java

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