Small classes and package reorganisation

opencb · Jun 25, 2020 · 45e7272 · 45e7272
1 parent 387ca11
commit 45e7272
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Showing 10 changed files with 55 additions and 46 deletions.
diff --git a/...a/formats/samtools/SamtoolsFlagstats.java → ...alignment/samtools/SamtoolsFlagstats.java b/...a/formats/samtools/SamtoolsFlagstats.java → ...alignment/samtools/SamtoolsFlagstats.java
@@ -1,4 +1,4 @@
-package org.opencb.biodata.formats.samtools;
+package org.opencb.biodata.formats.alignment.samtools;
 
 public class SamtoolsFlagstats {
 

diff --git a/...odata/formats/samtools/SamtoolsStats.java → ...ats/alignment/samtools/SamtoolsStats.java b/...odata/formats/samtools/SamtoolsStats.java → ...ats/alignment/samtools/SamtoolsStats.java
@@ -1,4 +1,4 @@
-package org.opencb.biodata.formats.samtools;
+package org.opencb.biodata.formats.alignment.samtools;
 
 public class SamtoolsStats {
 

diff --git a/...ical/qc/individual/InferredSexReport.java → ...models/clinical/qc/InferredSexReport.java b/...ical/qc/individual/InferredSexReport.java → ...models/clinical/qc/InferredSexReport.java
@@ -1,20 +1,23 @@
 /*
- * Copyright 2015-2020 OpenCB
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ Licensed under the Apache License, Version 2.0 (the "License");
+ *   ~ you may not use this file except in compliance with the License.
+ *   ~ You may obtain a copy of the License at
+ *   ~
+ *   ~     http://www.apache.org/licenses/LICENSE-2.0
+ *   ~
+ *   ~ Unless required by applicable law or agreed to in writing, software
+ *   ~ distributed under the License is distributed on an "AS IS" BASIS,
+ *   ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   ~ See the License for the specific language governing permissions and
+ *   ~ limitations under the License.
+ *   -->
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
  */
 
-package org.opencb.biodata.models.clinical.qc.individual;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;

diff --git a/...l/qc/individual/MendelianErrorReport.java → ...els/clinical/qc/MendelianErrorReport.java b/...l/qc/individual/MendelianErrorReport.java → ...els/clinical/qc/MendelianErrorReport.java
@@ -1,20 +1,23 @@
 /*
- * Copyright 2015-2020 OpenCB
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ Licensed under the Apache License, Version 2.0 (the "License");
+ *   ~ you may not use this file except in compliance with the License.
+ *   ~ You may obtain a copy of the License at
+ *   ~
+ *   ~     http://www.apache.org/licenses/LICENSE-2.0
+ *   ~
+ *   ~ Unless required by applicable law or agreed to in writing, software
+ *   ~ distributed under the License is distributed on an "AS IS" BASIS,
+ *   ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   ~ See the License for the specific language governing permissions and
+ *   ~ limitations under the License.
+ *   -->
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
  */
 
-package org.opencb.biodata.models.clinical.qc.individual;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...inical/qc/sample/MutationalSignature.java → ...dels/clinical/qc/MutationalSignature.java b/...inical/qc/sample/MutationalSignature.java → ...dels/clinical/qc/MutationalSignature.java
@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.models.clinical.qc.sample;
+package org.opencb.biodata.models.clinical.qc;
 
 public class MutationalSignature {
 

diff --git a/...ls/clinical/qc/sample/QcVariantStats.java → ...ta/models/clinical/qc/QcVariantStats.java b/...ls/clinical/qc/sample/QcVariantStats.java → ...ta/models/clinical/qc/QcVariantStats.java
@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.models.clinical.qc.sample;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.Map;
 

diff --git a/...ical/qc/individual/RelatednessReport.java → ...models/clinical/qc/RelatednessReport.java b/...ical/qc/individual/RelatednessReport.java → ...models/clinical/qc/RelatednessReport.java
@@ -1,20 +1,23 @@
 /*
- * Copyright 2015-2020 OpenCB
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ Licensed under the Apache License, Version 2.0 (the "License");
+ *   ~ you may not use this file except in compliance with the License.
+ *   ~ You may obtain a copy of the License at
+ *   ~
+ *   ~     http://www.apache.org/licenses/LICENSE-2.0
+ *   ~
+ *   ~ Unless required by applicable law or agreed to in writing, software
+ *   ~ distributed under the License is distributed on an "AS IS" BASIS,
+ *   ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   ~ See the License for the specific language governing permissions and
+ *   ~ limitations under the License.
+ *   -->
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
  */
 
-package org.opencb.biodata.models.clinical.qc.individual;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;

diff --git a/...nical/qc/sample/SampleQcVariantStats.java → ...els/clinical/qc/SampleQcVariantStats.java b/...nical/qc/sample/SampleQcVariantStats.java → ...els/clinical/qc/SampleQcVariantStats.java
@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.models.clinical.qc.sample;
+package org.opencb.biodata.models.clinical.qc;
 
 import org.opencb.biodata.models.variant.metadata.SampleVariantStats;
 

diff --git a/.../models/clinical/qc/sample/Signature.java → ...biodata/models/clinical/qc/Signature.java b/.../models/clinical/qc/sample/Signature.java → ...biodata/models/clinical/qc/Signature.java
@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.models.clinical.qc.sample;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.Arrays;
 import java.util.List;

diff --git a/.../clinical/qc/sample/SignatureFitting.java → .../models/clinical/qc/SignatureFitting.java b/.../clinical/qc/sample/SignatureFitting.java → .../models/clinical/qc/SignatureFitting.java
@@ -17,7 +17,7 @@
  *
  */
 
-package org.opencb.biodata.models.clinical.qc.sample;
+package org.opencb.biodata.models.clinical.qc;
 
 import java.util.Arrays;