public class CRAIIndex extends Object
Modifier and Type | Class and Description |
---|---|
static class |
CRAIIndex.CRAIIndexException |
Modifier and Type | Field and Description |
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static String |
CRAI_INDEX_SUFFIX |
Constructor and Description |
---|
CRAIIndex() |
Modifier and Type | Method and Description |
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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.
|
static CRAIEntry |
getLeftmost(List<CRAIEntry> list) |
static SeekableStream |
openCraiFileAsBaiStream(File cramIndexFile,
SAMSequenceDictionary dictionary) |
static SeekableStream |
openCraiFileAsBaiStream(InputStream indexStream,
SAMSequenceDictionary dictionary) |
static List<CRAIEntry> |
readIndex(InputStream is) |
static void |
writeIndex(OutputStream os,
List<CRAIEntry> index) |
public static final String CRAI_INDEX_SUFFIX
public static void writeIndex(OutputStream os, List<CRAIEntry> index) throws IOException
IOException
public static List<CRAIEntry> readIndex(InputStream is) throws CRAIIndex.CRAIIndexException
CRAIIndex.CRAIIndexException
public static int findLastAlignedEntry(List<CRAIEntry> list)
list
- a list of CRAI entriespublic static SeekableStream openCraiFileAsBaiStream(File cramIndexFile, SAMSequenceDictionary dictionary) throws IOException
IOException
public static SeekableStream openCraiFileAsBaiStream(InputStream indexStream, SAMSequenceDictionary dictionary) throws IOException, CRAIIndex.CRAIIndexException