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move protocol s3 from qio to qpicard #226

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move protocol s3 from qio to qpicard #226

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78d8bf3
move protocol s3 from qio to qpicard
ChristinaXu2017 Jan 27, 2021
cf36581
move qio from qtesting, qmotif and qpicard
ChristinaXu2017 Jan 28, 2021
6d7c833
move class QSnpRecord from qio to qcommon
ChristinaXu2017 Jan 28, 2021
4c6124a
update since QSnpRecord relocation
ChristinaXu2017 Jan 28, 2021
6a2a83b
update due to QSnpRcord relocation
ChristinaXu2017 Jan 28, 2021
fba5de5
delete empty unit test class
ChristinaXu2017 Jan 28, 2021
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6 changes: 1 addition & 5 deletions qio/src/org/qcmg/pileup/QSnpRecord.java → ...src/org/qcmg/common/model/QSnpRecord.java
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Expand Up @@ -4,13 +4,9 @@
*
* This code is released under the terms outlined in the included LICENSE file.
*/
package org.qcmg.pileup;
package org.qcmg.common.model;


import org.qcmg.common.model.Accumulator;
import org.qcmg.common.model.ChrPosition;
import org.qcmg.common.model.Classification;
import org.qcmg.common.model.GenotypeEnum;
import org.qcmg.common.vcf.VcfRecord;

@Deprecated
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1 change: 0 additions & 1 deletion qmotif/build.gradle
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Expand Up @@ -10,7 +10,6 @@ repositories { mavenCentral() }
dependencies {
configurations.compile.transitive = true
api project(':qcommon')
api project(':qio')
api project(':qbamfilter')
api project(':qpicard')

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1 change: 0 additions & 1 deletion qpicard/build.gradle
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Expand Up @@ -3,7 +3,6 @@ def isExecutable = false
dependencies {
configurations.compile.transitive = true
api project(':qcommon')
api project(':qio')

api 'com.github.broadinstitute:picard:1.130'
api 'com.github.samtools:htsjdk:2.14.1'
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2 changes: 1 addition & 1 deletion qpicard/src/org/qcmg/picard/SAMFileReaderFactory.java
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Expand Up @@ -27,7 +27,7 @@
import org.qcmg.common.log.QLogger;
import org.qcmg.common.log.QLoggerFactory;
import org.qcmg.common.string.StringUtils;
import org.qcmg.protocol.s3.S3AwareURLStreamHandlerFactory;
import org.qcmg.picard.s3.S3AwareURLStreamHandlerFactory;
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I really don't understand this move. The s3 package is for low-level AWS operations - for example, all it ever throws is IOException. picard is specifically for handling fastq/bam/sam sequence data which is a way more specialized task. By moving this out of qio into qpicard that means any time I want to access ANY s3 file stream, whether it contains a VCF, text or whatever, I have to import a sequence data handling package. That just seems wrong to me.
A lot of my reluctance I think comes from my (very imperfect) understanding of what problem this is attempting to solve. It seems like if the issue is multiple paths to the same dependency, that is something that should be fixed in the build configuration (with excludes) rather than restructuring packages themselves.


public class SAMFileReaderFactory {
// EnumSet<Option> defultOption = SamReaderFactory.Option.DEFAULTS;
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2 changes: 1 addition & 1 deletion ...ol/s3/S3AwareURLStreamHandlerFactory.java → ...rd/s3/S3AwareURLStreamHandlerFactory.java
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@@ -1,4 +1,4 @@
package org.qcmg.protocol.s3;
package org.qcmg.picard.s3;

import java.net.URLStreamHandler;
import java.net.URLStreamHandlerFactory;
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2 changes: 1 addition & 1 deletion ...org/qcmg/protocol/s3/S3URLConnection.java → ...c/org/qcmg/picard/s3/S3URLConnection.java
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@@ -1,4 +1,4 @@
package org.qcmg.protocol.s3;
package org.qcmg.picard.s3;

import java.io.IOException;
import java.io.InputStream;
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2 changes: 1 addition & 1 deletion .../qcmg/protocol/s3/S3URLStreamHandler.java → ...rg/qcmg/picard/s3/S3URLStreamHandler.java
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@@ -1,4 +1,4 @@
package org.qcmg.protocol.s3;
package org.qcmg.picard.s3;

import java.io.IOException;
import java.net.URL;
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2 changes: 1 addition & 1 deletion qsnp/src/org/qcmg/snp/MuTectPipeline.java
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Expand Up @@ -36,7 +36,7 @@
import org.qcmg.common.vcf.VcfRecord;
import org.qcmg.picard.SAMFileReaderFactory;
import org.qcmg.picard.util.SAMUtils;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;
import org.qcmg.common.model.Classification;
import org.qcmg.snp.util.IniFileUtil;
import org.qcmg.tab.TabbedFileReader;
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2 changes: 1 addition & 1 deletion qsnp/src/org/qcmg/snp/PileupPipeline.java
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Expand Up @@ -21,7 +21,7 @@
import org.qcmg.common.model.ChrPosition;
import org.qcmg.common.string.StringUtils;
import org.qcmg.pileup.PileupFileReader;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;
import org.qcmg.common.model.Classification;
import org.qcmg.snp.util.IniFileUtil;
import org.qcmg.snp.util.QJumperWorker;
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2 changes: 1 addition & 1 deletion qsnp/src/org/qcmg/snp/TorrentPipeline.java
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Expand Up @@ -28,7 +28,7 @@
import org.qcmg.picard.QJumper;
import org.qcmg.picard.util.PileupElementUtil;
import org.qcmg.picard.util.SAMUtils;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;
import org.qcmg.snp.filters.AdjacentIndelFilter;
import org.qcmg.snp.filters.EndOfReadFilter;
import org.qcmg.snp.filters.MultipleAdjacentSnpsFilter;
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2 changes: 1 addition & 1 deletion qsnp/src/org/qcmg/snp/util/BAMPileupUtil.java
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Expand Up @@ -18,7 +18,7 @@
import org.qcmg.common.model.QSnpGATKRecord;
import org.qcmg.picard.util.PileupElementUtil;
import org.qcmg.picard.util.SAMUtils;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;
import org.qcmg.snp.util.QJumperWorker.Mode;

public class BAMPileupUtil {
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2 changes: 1 addition & 1 deletion qsnp/src/org/qcmg/snp/util/QJumperWorker.java
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Expand Up @@ -14,7 +14,7 @@
import org.qcmg.common.log.QLoggerFactory;
import org.qcmg.common.model.QSnpGATKRecord;
import org.qcmg.picard.QJumper;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;

public class QJumperWorker<T> implements Runnable {

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2 changes: 1 addition & 1 deletion qsnp/test/org/qcmg/snp/util/BAMPileupUtilTest.java
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Expand Up @@ -12,7 +12,7 @@
import org.qcmg.common.util.SnpUtils;
import org.qcmg.common.vcf.VcfRecord;
import org.qcmg.common.vcf.VcfUtils;
import org.qcmg.pileup.QSnpRecord;
import org.qcmg.common.model.QSnpRecord;
import org.qcmg.snp.util.QJumperWorker.Mode;

public class BAMPileupUtilTest {
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1 change: 0 additions & 1 deletion qtesting/build.gradle
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Expand Up @@ -2,7 +2,6 @@ def isExecutable = false

dependencies {
configurations.compile.transitive = true
api project(':qio')
api project(':qcommon')
}