Class
TabixIndexAccess to Tabix indexed files.
Access to Tabix indexed files.
Defined in | <seqan/tabix_io.h> |
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Signature |
class TabixIndex;
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Member Function Overview
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TabixIndex::TabixIndex();
Constructor.
Interface Function Overview
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uint64_t getUnalignedCount(index);
Query index for number of unaligned reads. -
bool jumpToRegion(fileIn, hasEntries, refName, posBeg, posEnd, index[, firstMatch]);
Seek in a tab-separated genome related file using a Tabix index. -
bool open(index, filename);
Load a Tabix index from file.
Member Functions Detail
TabixIndex::TabixIndex();
Constructor.
Remarks
Only the default constructor is provided.
Data Races
Thread safety unknown!
Interface Functions Detail
uint64_t getUnalignedCount(index);
Query index for number of unaligned reads.
Parameters
index
|
Index to query. |
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Returns
uint64_t |
The number of unaligned reads. |
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Data Races
Thread safety unknown!
bool jumpToRegion(fileIn, hasEntries, refName, posBeg, posEnd, index[, firstMatch]);
Seek in a tab-separated genome related file using a Tabix index.
Parameters
fileIn
|
The VcfFileIn, GffFileIn, or BedFileIn to jump with. |
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hasEntries
|
A bool that is set true if the region [posBeg, posEnd) has any entries. |
refName
|
The reference name to jump to. |
posBeg
|
The begin of the region to jump to (int32_t). |
posEnd
|
The end of the region to jump to (int32_t). |
index
|
The TabixIndex to use for the jumping. |
firstMatch
|
A bool, if true (default) this function seeks to the first overlapping record. Otherwise, the function potentially stops before the first overlapping record. |
Returns
bool |
true if seeking was successful, false if not. |
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You provide a region [posBeg, posEnd) on the contig refName that you want to jump to and the function jumps to the first entry in this region, if any.
Remarks
This function fails if refName/pos wasn't found.
Data Races
Thread safety unknown!
bool open(index, filename);
Load a Tabix index from file.
Parameters
index
|
Target data structure. |
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filename
|
Path to file to load. Types: char const * |
Returns
bool |
Returns true on success, false otherwise. |
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Data Races
Thread safety unknown!