public class CRAIIndex
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
CRAIIndex.CRAIIndexException |
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
CRAI_INDEX_SUFFIX |
Constructor and Description |
---|
CRAIIndex() |
Modifier and Type | Method and Description |
---|---|
static java.util.List<CRAIEntry> |
find(java.util.List<CRAIEntry> list,
int seqId,
int start,
int span) |
static int |
findLastAlignedEntry(java.util.List<CRAIEntry> list)
Find index of the last aligned entry in the list.
|
static CRAIEntry |
getLeftmost(java.util.List<CRAIEntry> list) |
static SeekableStream |
openCraiFileAsBaiStream(java.io.File cramIndexFile,
SAMSequenceDictionary dictionary) |
static SeekableStream |
openCraiFileAsBaiStream(java.io.InputStream indexStream,
SAMSequenceDictionary dictionary) |
static java.util.List<CRAIEntry> |
readIndex(java.io.InputStream is) |
static void |
writeIndex(java.io.OutputStream os,
java.util.List<CRAIEntry> index) |
public static final java.lang.String CRAI_INDEX_SUFFIX
public static void writeIndex(java.io.OutputStream os, java.util.List<CRAIEntry> index) throws java.io.IOException
java.io.IOException
public static java.util.List<CRAIEntry> readIndex(java.io.InputStream is) throws CRAIIndex.CRAIIndexException
CRAIIndex.CRAIIndexException
public static java.util.List<CRAIEntry> find(java.util.List<CRAIEntry> list, int seqId, int start, int span)
public static int findLastAlignedEntry(java.util.List<CRAIEntry> list)
list
- a list of CRAI entriespublic static SeekableStream openCraiFileAsBaiStream(java.io.File cramIndexFile, SAMSequenceDictionary dictionary) throws java.io.IOException
java.io.IOException
public static SeekableStream openCraiFileAsBaiStream(java.io.InputStream indexStream, SAMSequenceDictionary dictionary) throws java.io.IOException, CRAIIndex.CRAIIndexException
java.io.IOException
CRAIIndex.CRAIIndexException