FaiIndex

Include Headers

seqan/seq_io.h

Data Members

The FaiIndex class only provides the default constructor.

Functions

build	Create FaiIndex from FASTA file.
clear	Reset a FaiIndex object to the state after default construction.
getIdByName	Return id (numeric index in the file) of a sequence in a FAI file.
numSeqs	Return number of sequences known to an FaiIndex.
read	Read a FAI index.
readRegion	Load the infix of a sequence from a FaiIndex.
readSequence	Load a whole sequence from an FaiIndex.
sequenceLength	Return length of the sequence with the given id in the FaiIndex.
sequenceName	Return the name of the sequence with the given id in the FaiIndex.
write	Write out an FaiIndex object.

Examples

The following example demonstrate the usage of the FAIIndex class.

1	#include <seqan/basic.h>
2	#include <seqan/seq_io.h>
3	#include <seqan/sequence.h>
4
5	using namespace seqan;
6
7	int main(int argc, char ** argv)
8	{
9	if (argc != 2)
10	{
11	std::cerr << "USAGE: " << argv[0] << " SEQUENCE.fasta\n";
12	return 1;
13	}
14
15	FaiIndex faiIndex;
16
17	// Try to read the FAI index.
18	bool readSuccess = (read(faiIndex, argv[1]) == 0);
19	if (!readSuccess)
20	std::cerr << "Could not read the FAI index. Not fatal, we can just build it.\n";
21
22	// Try to build the FAI index (in memory) if reading was unsuccessful. If
23	// building into memory succeeded, we try to write it out.
24	if (!readSuccess)
25	{
26	if (build(faiIndex, argv[1]) != 0)
27	{
28	std::cerr << "FATAL: Could not build FAI index.\n";
29	return 1;
30	}
31
32	if (write(faiIndex) != 0)
33	{
34	std::cerr << "FATAL: Could not write out FAI index after building.\n";
35	return 1;
36	}
37	}
38
39	// Now, read the first 1000 characters of chr1.
40	unsigned idx = 0;
41	if (!getIdByName(faiIndex, "chr1", idx))
42	{
43	std::cerr << "FATAL: chr1 not found in FAI index.\n";
44	return 1;
45	}
46	CharString seq;
47	if (readRegion(seq, faiIndex, idx, 0, 1000) != 0)
48	{
49	std::cerr << "FATAL: Problem reading FASTA file through FAI index.\n";
50	return 1;
51	}
52
53	// Now print the first 1000 characters we just read.
54	std::cerr << "chr1:1-1000 = " << seq << "\n";
55
56	return 0;
57	}