From 3ce3e27aa1bd2dfd0fafee536e33a119a6693ab0 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Wed, 7 May 2014 12:50:28 +0800 Subject: [PATCH] Moved GATK classes and POMs that will need updating. GATK classes accessing package protected htsjdk classes will need new package names. POMs will merge sam/tribble/variant into htsjdk. Move only, contents updated in next commit. First of four commits for picard/htsjdk package rename. --- .../main/java/{net/sf => htsjdk}/samtools/GATKBAMFileSpan.java | 0 .../src/main/java/{net/sf => htsjdk}/samtools/GATKBin.java | 0 .../src/main/java/{net/sf => htsjdk}/samtools/GATKChunk.java | 0 .../java/{net/sf => htsjdk}/samtools/PicardNamespaceUtils.java | 0 .../java/{net/sf => htsjdk}/samtools/GATKBAMFileSpanUnitTest.java | 0 .../test/java/{net/sf => htsjdk}/samtools/GATKChunkUnitTest.java | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename public/gatk-framework/src/main/java/{net/sf => htsjdk}/samtools/GATKBAMFileSpan.java (100%) rename public/gatk-framework/src/main/java/{net/sf => htsjdk}/samtools/GATKBin.java (100%) rename public/gatk-framework/src/main/java/{net/sf => htsjdk}/samtools/GATKChunk.java (100%) rename public/gatk-framework/src/main/java/{net/sf => htsjdk}/samtools/PicardNamespaceUtils.java (100%) rename public/gatk-framework/src/test/java/{net/sf => htsjdk}/samtools/GATKBAMFileSpanUnitTest.java (100%) rename public/gatk-framework/src/test/java/{net/sf => htsjdk}/samtools/GATKChunkUnitTest.java (100%) diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java similarity index 100% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBin.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java similarity index 100% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKBin.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKChunk.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java similarity index 100% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKChunk.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/PicardNamespaceUtils.java b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java similarity index 100% rename from public/gatk-framework/src/main/java/net/sf/samtools/PicardNamespaceUtils.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java diff --git a/public/gatk-framework/src/test/java/net/sf/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/net/sf/samtools/GATKBAMFileSpanUnitTest.java rename to public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java diff --git a/public/gatk-framework/src/test/java/net/sf/samtools/GATKChunkUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java similarity index 100% rename from public/gatk-framework/src/test/java/net/sf/samtools/GATKChunkUnitTest.java rename to public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java