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Reformat source code for consistent code style #154

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Reformat source code for consistent code style #154

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9293243
Reformat source code for consistent use of whitespace.
heuermh Sep 11, 2017
4cc7b01
Make method parameters final where possible.
heuermh Sep 12, 2017
9195287
Fixup whitespace missed or caused by formatter.
heuermh Sep 12, 2017
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32 changes: 32 additions & 0 deletions etc/IntelliJ IDEA Code Style.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
<code_scheme name="Default (1)">
<option name="CLASS_COUNT_TO_USE_IMPORT_ON_DEMAND" value="99" />
<option name="NAMES_COUNT_TO_USE_IMPORT_ON_DEMAND" value="99" />
<option name="IMPORT_LAYOUT_TABLE">
<value>
<package name="java" withSubpackages="true" static="false" />
<package name="javax" withSubpackages="true" static="false" />
<package name="" withSubpackages="true" static="false" />
<emptyLine />
<emptyLine />
<package name="" withSubpackages="true" static="true" />
</value>
</option>
<option name="JD_ALIGN_PARAM_COMMENTS" value="false" />
<option name="JD_ALIGN_EXCEPTION_COMMENTS" value="false" />
<ScalaCodeStyleSettings>
<option name="USE_SCALADOC2_FORMATTING" value="false" />
<option name="ENABLE_SCALADOC_FORMATTING" value="false" />
</ScalaCodeStyleSettings>
<codeStyleSettings language="JAVA">
<option name="ELSE_ON_NEW_LINE" value="true" />
<option name="WHILE_ON_NEW_LINE" value="true" />
<option name="CATCH_ON_NEW_LINE" value="true" />
<option name="FINALLY_ON_NEW_LINE" value="true" />
<option name="SPACE_WITHIN_ARRAY_INITIALIZER_BRACES" value="true" />
<option name="SPACE_BEFORE_ARRAY_INITIALIZER_LBRACE" value="true" />
<option name="IF_BRACE_FORCE" value="3" />
<option name="DOWHILE_BRACE_FORCE" value="3" />
<option name="WHILE_BRACE_FORCE" value="3" />
<option name="FOR_BRACE_FORCE" value="3" />
</codeStyleSettings>
</code_scheme>
5 changes: 1 addition & 4 deletions examples/src/main/java/org/seqdoop/hadoop_bam/examples/TestBAM.java
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Expand Up @@ -22,7 +22,7 @@

import java.io.IOException;
import java.util.Iterator;

import htsjdk.samtools.SAMRecord;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
Expand All @@ -34,9 +34,6 @@
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;

import htsjdk.samtools.SAMRecord;

import org.seqdoop.hadoop_bam.AnySAMInputFormat;
import org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat;
import org.seqdoop.hadoop_bam.SAMRecordWritable;
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5 changes: 1 addition & 4 deletions examples/src/main/java/org/seqdoop/hadoop_bam/examples/TestVCF.java
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Expand Up @@ -22,7 +22,7 @@

import java.io.IOException;
import java.util.Iterator;

import htsjdk.variant.variantcontext.VariantContext;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
Expand All @@ -34,9 +34,6 @@
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;

import htsjdk.variant.variantcontext.VariantContext;

import org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat;
import org.seqdoop.hadoop_bam.VCFInputFormat;
import org.seqdoop.hadoop_bam.VCFOutputFormat;
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17 changes: 7 additions & 10 deletions src/main/java/htsjdk/samtools/LinearBAMIndex.java
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Expand Up @@ -19,21 +19,18 @@
// IN THE SOFTWARE.
package htsjdk.samtools;

import htsjdk.samtools.CachingBAMFileIndex;
import htsjdk.samtools.LinearIndex;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.seekablestream.SeekableStream;

/**
* The htsjdk APIs for accessing the linear BAM index are private...
*/
public class LinearBAMIndex extends CachingBAMFileIndex {

public LinearBAMIndex(SeekableStream stream, SAMSequenceDictionary dict) {
super(stream, dict);
}
public LinearIndex getLinearIndex(int idx) {
return getQueryResults(idx).getLinearIndex();
}
public LinearBAMIndex(final SeekableStream stream, final SAMSequenceDictionary dict) {
super(stream, dict);
}

public LinearIndex getLinearIndex(final int idx) {
return getQueryResults(idx).getLinearIndex();
}
}
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