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Add an IntervalCodec that use useful for sorting large sets of Interv…
…als (#1288) * Added IntervalCodec that is useful for sorting large sets of Intervals. * Made IntervalCoordinateComparator public * Adding an IntervalListWriter class to write Intervals.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2019 Nils Homer | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| */ | ||
| package htsjdk.samtools.util; | ||
|
|
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| import htsjdk.samtools.SAMSequenceDictionary; | ||
| import java.io.InputStream; | ||
| import java.io.OutputStream; | ||
|
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| public class IntervalCodec implements SortingCollection.Codec<Interval> { | ||
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| private final SAMSequenceDictionary dict; | ||
|
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| private final BinaryCodec binaryCodec = new BinaryCodec(); | ||
|
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| /** | ||
| * Creates a new binary codec to read or write. | ||
| * @param dict the sequence dictionary associated with the intervals. | ||
| */ | ||
| public IntervalCodec(final SAMSequenceDictionary dict) { | ||
| this.dict = dict; | ||
| } | ||
|
|
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| @Override | ||
| public IntervalCodec clone() { | ||
| return new IntervalCodec(this.dict); | ||
| } | ||
|
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|
|
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| /** | ||
| * Sets the output stream that records will be written to. | ||
| */ | ||
| @Override | ||
| public void setOutputStream(final OutputStream os) { | ||
| this.binaryCodec.setOutputStream(os); | ||
| } | ||
|
|
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| /** | ||
| * Sets the output stream that records will be written to. | ||
| */ | ||
| public void setOutputStream(final OutputStream os, final String filename) { | ||
| this.binaryCodec.setOutputStream(os); | ||
| this.binaryCodec.setOutputFileName(filename); | ||
| } | ||
|
|
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| /** | ||
| * Sets the input stream that records will be read from. | ||
| */ | ||
| @Override | ||
| public void setInputStream(final InputStream is) { | ||
| this.binaryCodec.setInputStream(is); | ||
| } | ||
|
|
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| /** | ||
| * Sets the input stream that records will be read from. | ||
| */ | ||
| public void setInputStream(final InputStream is, final String filename) { | ||
| this.binaryCodec.setInputStream(is); | ||
| this.binaryCodec.setInputFileName(filename); | ||
| } | ||
|
|
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| /** | ||
| * Writes the interval to the output stream. | ||
| * @param interval the interval to write. | ||
| */ | ||
| @Override | ||
| public void encode(final Interval interval) { | ||
| final String name = interval.getName(); | ||
| this.binaryCodec.writeInt(this.dict.getSequenceIndex(interval.getContig())); | ||
| this.binaryCodec.writeInt(interval.getStart()); | ||
| this.binaryCodec.writeInt(interval.getEnd()); | ||
| this.binaryCodec.writeBoolean(interval.isNegativeStrand()); | ||
| this.binaryCodec.writeBoolean(name != null); | ||
| if (name != null) { | ||
| this.binaryCodec.writeString(name, false, true); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Reads an interval from the input stream. | ||
| * @return null if no more intervals, otherwise the next interval. | ||
| */ | ||
| @Override | ||
| public Interval decode() { | ||
| final int sequenceIndex; | ||
| try { | ||
| sequenceIndex = this.binaryCodec.readInt(); | ||
| } catch (final RuntimeEOFException e) { | ||
| return null; | ||
| } | ||
| return new Interval( | ||
| this.dict.getSequence(sequenceIndex).getSequenceName(), | ||
| this.binaryCodec.readInt(), | ||
| this.binaryCodec.readInt(), | ||
| this.binaryCodec.readBoolean(), | ||
| (this.binaryCodec.readBoolean()) ? this.binaryCodec.readNullTerminatedString() : null | ||
| ); | ||
| } | ||
| } |
80 changes: 80 additions & 0 deletions
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src/main/java/htsjdk/samtools/util/IntervalCoordinateComparator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2019 Nils Homer | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| */ | ||
| package htsjdk.samtools.util; | ||
|
|
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| import htsjdk.samtools.SAMFileHeader; | ||
|
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| import java.io.Serializable; | ||
| import java.util.Comparator; | ||
|
|
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| /** | ||
| * Comparator that orders intervals based on their sequence index, by coordinate | ||
| * then by strand and finally by name. | ||
| */ | ||
| public class IntervalCoordinateComparator implements Comparator<Interval>, Serializable { | ||
| private static final long serialVersionUID = 1L; | ||
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| private final SAMFileHeader header; | ||
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| /** Constructs a comparator using the supplied sequence header. */ | ||
| public IntervalCoordinateComparator(final SAMFileHeader header) { | ||
| this.header = header; | ||
| } | ||
|
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| @Override | ||
| public int compare(final Interval lhs, final Interval rhs) { | ||
| final int lhsIndex = this.header.getSequenceIndex(lhs.getContig()); | ||
| final int rhsIndex = this.header.getSequenceIndex(rhs.getContig()); | ||
| int retval = lhsIndex - rhsIndex; | ||
|
|
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| if (retval == 0) { | ||
| retval = lhs.getStart() - rhs.getStart(); | ||
| } | ||
| if (retval == 0) { | ||
| retval = lhs.getEnd() - rhs.getEnd(); | ||
| } | ||
| if (retval == 0) { | ||
| if (lhs.isPositiveStrand() && rhs.isNegativeStrand()) { | ||
| retval = -1; | ||
| } else if (lhs.isNegativeStrand() && rhs.isPositiveStrand()) { | ||
| retval = 1; | ||
| } | ||
| } | ||
| if (retval == 0) { | ||
| if (lhs.getName() == null) { | ||
| if (rhs.getName() == null) { | ||
| return 0; | ||
| } else { | ||
| return -1; | ||
| } | ||
| } else if (rhs.getName() == null) { | ||
| return 1; | ||
| } else { | ||
| return lhs.getName().compareTo(rhs.getName()); | ||
| } | ||
| } | ||
|
|
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| return retval; | ||
| } | ||
| } |
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