Class TabixIndex
Access to Tabix indexed files.

Defined in <seqan/tabix_io.h>
Signature class TabixIndex;

Member Function Overview

Interface Function Overview

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.

Returns

uint64_t The number of unaligned reads.

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.
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.

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.
filename Path to file to load. Types: char const *

Returns

bool Returns true on success, false otherwise.

Data Races

Thread safety unknown!