From 2c16c18a046e2999cb5ab28d140a33fffa5525f9 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 1 Dec 2009 05:29:00 +0000 Subject: [PATCH] Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/multisamplecaller}/MultiSampleCallerAccuracyTest.java | 0 .../org/broadinstitute/sting/oldindels}/ConsensusSequence.java | 0 .../broadinstitute/sting/oldindels}/DiscardingPileReceiver.java | 0 .../org/broadinstitute/sting/oldindels}/DiscardingReceiver.java | 0 .../java/src/org/broadinstitute/sting/oldindels}/Indel.java | 0 .../org/broadinstitute/sting/oldindels}/IndelInspectorMain.java | 0 .../broadinstitute/sting/oldindels}/IndelRecordPileCollector.java | 0 .../src/org/broadinstitute/sting/oldindels}/IndexedSequence.java | 0 .../org/broadinstitute/sting/oldindels}/IntervalComparator.java | 0 .../src/org/broadinstitute/sting/oldindels}/KmerCodeIterator.java | 0 .../java/src/org/broadinstitute/sting/oldindels}/MSAColumn.java | 0 .../java/src/org/broadinstitute/sting/oldindels}/Matrix.java | 0 .../org/broadinstitute/sting/oldindels}/MultipleAlignment.java | 0 .../org/broadinstitute/sting/oldindels}/PairwiseAlignment.java | 0 .../org/broadinstitute/sting/oldindels}/PassThroughWriter.java | 0 .../java/src/org/broadinstitute/sting/oldindels}/PileBuilder.java | 0 .../org/broadinstitute/sting/oldindels}/RecordPileReceiver.java | 0 .../src/org/broadinstitute/sting/oldindels}/RecordReceiver.java | 0 .../src/org/broadinstitute/sting/oldindels}/SequencePile.java | 0 .../java/src/org/broadinstitute/sting/oldindels}/ShowMSA.java | 0 .../sting/oldindels}/StrictlyUpperTriangularMatrix.java | 0 .../src/org/broadinstitute/sting/oldindels}/SymmetricMatrix.java | 0 22 files changed, 0 insertions(+), 0 deletions(-) rename {java/src/org/broadinstitute/sting/playground/gatk/walkers => archive/java/src/org/broadinstitute/sting/multisamplecaller}/MultiSampleCallerAccuracyTest.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/ConsensusSequence.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/DiscardingPileReceiver.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/DiscardingReceiver.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/Indel.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/IndelInspectorMain.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/IndelRecordPileCollector.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/IndexedSequence.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/IntervalComparator.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/KmerCodeIterator.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/MSAColumn.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/Matrix.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/MultipleAlignment.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/PairwiseAlignment.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/PassThroughWriter.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/PileBuilder.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/RecordPileReceiver.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/RecordReceiver.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/SequencePile.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/ShowMSA.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/StrictlyUpperTriangularMatrix.java (100%) rename {java/src/org/broadinstitute/sting/playground/indels => archive/java/src/org/broadinstitute/sting/oldindels}/SymmetricMatrix.java (100%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCallerAccuracyTest.java b/archive/java/src/org/broadinstitute/sting/multisamplecaller/MultiSampleCallerAccuracyTest.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCallerAccuracyTest.java rename to archive/java/src/org/broadinstitute/sting/multisamplecaller/MultiSampleCallerAccuracyTest.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java b/archive/java/src/org/broadinstitute/sting/oldindels/ConsensusSequence.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java rename to archive/java/src/org/broadinstitute/sting/oldindels/ConsensusSequence.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/DiscardingPileReceiver.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java rename to archive/java/src/org/broadinstitute/sting/oldindels/DiscardingPileReceiver.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/DiscardingReceiver.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java rename to archive/java/src/org/broadinstitute/sting/oldindels/DiscardingReceiver.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/Indel.java b/archive/java/src/org/broadinstitute/sting/oldindels/Indel.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/Indel.java rename to archive/java/src/org/broadinstitute/sting/oldindels/Indel.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndelInspectorMain.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java rename to archive/java/src/org/broadinstitute/sting/oldindels/IndelInspectorMain.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndelRecordPileCollector.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java rename to archive/java/src/org/broadinstitute/sting/oldindels/IndelRecordPileCollector.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndexedSequence.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java rename to archive/java/src/org/broadinstitute/sting/oldindels/IndexedSequence.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java b/archive/java/src/org/broadinstitute/sting/oldindels/IntervalComparator.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java rename to archive/java/src/org/broadinstitute/sting/oldindels/IntervalComparator.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java b/archive/java/src/org/broadinstitute/sting/oldindels/KmerCodeIterator.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java rename to archive/java/src/org/broadinstitute/sting/oldindels/KmerCodeIterator.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java b/archive/java/src/org/broadinstitute/sting/oldindels/MSAColumn.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java rename to archive/java/src/org/broadinstitute/sting/oldindels/MSAColumn.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/Matrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/Matrix.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/Matrix.java rename to archive/java/src/org/broadinstitute/sting/oldindels/Matrix.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java b/archive/java/src/org/broadinstitute/sting/oldindels/MultipleAlignment.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java rename to archive/java/src/org/broadinstitute/sting/oldindels/MultipleAlignment.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java b/archive/java/src/org/broadinstitute/sting/oldindels/PairwiseAlignment.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java rename to archive/java/src/org/broadinstitute/sting/oldindels/PairwiseAlignment.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/PassThroughWriter.java b/archive/java/src/org/broadinstitute/sting/oldindels/PassThroughWriter.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/PassThroughWriter.java rename to archive/java/src/org/broadinstitute/sting/oldindels/PassThroughWriter.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java b/archive/java/src/org/broadinstitute/sting/oldindels/PileBuilder.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java rename to archive/java/src/org/broadinstitute/sting/oldindels/PileBuilder.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/RecordPileReceiver.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java rename to archive/java/src/org/broadinstitute/sting/oldindels/RecordPileReceiver.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/RecordReceiver.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java rename to archive/java/src/org/broadinstitute/sting/oldindels/RecordReceiver.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/SequencePile.java b/archive/java/src/org/broadinstitute/sting/oldindels/SequencePile.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/SequencePile.java rename to archive/java/src/org/broadinstitute/sting/oldindels/SequencePile.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java b/archive/java/src/org/broadinstitute/sting/oldindels/ShowMSA.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java rename to archive/java/src/org/broadinstitute/sting/oldindels/ShowMSA.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/StrictlyUpperTriangularMatrix.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java rename to archive/java/src/org/broadinstitute/sting/oldindels/StrictlyUpperTriangularMatrix.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/SymmetricMatrix.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java rename to archive/java/src/org/broadinstitute/sting/oldindels/SymmetricMatrix.java