broad.core.sequence.FastaQualityBinaryIO Class Reference

Public Member Functions
void	createBinaryFromAscii (InputStream in, String outFile) throws IOException
void	toDBFromAscii (InputStream in, final Connection conn, String table) throws IOException, SQLException
void	createAsciiFromBinary (String binaryQualityFile, int numQualBasesPerRow) throws IOException
int[]	getQualityBases (Connection conn, String table, String seqId, int start, int numOfBases) throws SQLException
int[]	getQualityBases (Connection conn, String table, String seqId) throws SQLException

Static Public Attributes
static final int	SEQ_ID_REC_LENGTH = 300
static final int	BUFFER_SIZE = 8192

Member Function Documentation

void broad.core.sequence.FastaQualityBinaryIO.createAsciiFromBinary	(	String	binaryQualityFile,
		int	numQualBasesPerRow
	)		throws IOException

void broad.core.sequence.FastaQualityBinaryIO.createBinaryFromAscii	(	InputStream	in,
		String	outFile
	)		throws IOException

Here is the call graph for this function:

int [] broad.core.sequence.FastaQualityBinaryIO.getQualityBases	(	Connection	conn,
		String	table,
		String	seqId,
		int	start,
		int	numOfBases
	)		throws SQLException

Retrieves quality base calls for a given sequence from a binary quality assembly file.

Parameters

Table	- Database table containing the assembly quality info.
seqId	- Sequence id of interest.
start	- Zero based start of base (included)
numOfBases	- number of bases to retrieve starting from base start.

Returns

Exceptions

SQLException

int [] broad.core.sequence.FastaQualityBinaryIO.getQualityBases	(	Connection	conn,
		String	table,
		String	seqId
	)		throws SQLException

Retrieves quality base calls for a given sequence from a binary quality assembly file. Use wisely, it returns an integer array with ALL quality scores.

Parameters

Table	- Database table containing the assembly quality info.
seqId	- Sequence id of interest.

Returns

Exceptions

SQLException

void broad.core.sequence.FastaQualityBinaryIO.toDBFromAscii	(	InputStream	in,
		final Connection	conn,
		String	table
	)		throws IOException, SQLException

Member Data Documentation

final int broad.core.sequence.FastaQualityBinaryIO.BUFFER_SIZE = 8192

static

final int broad.core.sequence.FastaQualityBinaryIO.SEQ_ID_REC_LENGTH = 300

static

---

The documentation for this class was generated from the following file:

• java/broad/core/sequence/FastaQualityBinaryIO.java