Package htsjdk.samtools.cram
Class CRAIIndex
- java.lang.Object
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- htsjdk.samtools.cram.CRAIIndex
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public class CRAIIndex extends Object
CRAI index used for CRAM files.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CRAIIndex.CRAIIndexException
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Field Summary
Fields Modifier and Type Field Description static String
CRAI_INDEX_SUFFIX
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Constructor Summary
Constructors Constructor Description CRAIIndex()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addEntry(CRAIEntry entry)
Add a single entry to the CRAI index.static List<CRAIEntry>
find(List<CRAIEntry> list, int seqId, int start, int span)
static int
findLastAlignedEntry(List<CRAIEntry> list)
Find index of the last aligned entry in the list.List<CRAIEntry>
getCRAIEntries()
static CRAIEntry
getLeftmost(List<CRAIEntry> list)
static SeekableStream
openCraiFileAsBaiStream(File cramIndexFile, SAMSequenceDictionary dictionary)
static SeekableStream
openCraiFileAsBaiStream(InputStream indexStream, SAMSequenceDictionary dictionary)
void
processContainer(Container c)
Create index entries for a single container.void
writeIndex(OutputStream os)
Write out the index to an output stream;
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Field Detail
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CRAI_INDEX_SUFFIX
public static final String CRAI_INDEX_SUFFIX
- See Also:
- Constant Field Values
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Method Detail
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addEntry
public void addEntry(CRAIEntry entry)
Add a single entry to the CRAI index.- Parameters:
entry
- entry to be added
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writeIndex
public void writeIndex(OutputStream os)
Write out the index to an output stream;- Parameters:
os
- Stream to write index to
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processContainer
public void processContainer(Container c)
Create index entries for a single container.- Parameters:
c
- the container to index
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openCraiFileAsBaiStream
public static SeekableStream openCraiFileAsBaiStream(File cramIndexFile, SAMSequenceDictionary dictionary) throws IOException
- Throws:
IOException
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openCraiFileAsBaiStream
public static SeekableStream openCraiFileAsBaiStream(InputStream indexStream, SAMSequenceDictionary dictionary) throws IOException, CRAIIndex.CRAIIndexException
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findLastAlignedEntry
public static int findLastAlignedEntry(List<CRAIEntry> list)
Find index of the last aligned entry in the list. Assumes the index is sorted by coordinate and unmapped entries (with sequence id = -1) follow the mapped entries.- Parameters:
list
- a list of CRAI entries- Returns:
- integer index of the last entry with sequence id not equal to -1
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