Documentation
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Index ¶
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func DifferentBarcode ¶
* Decide of two reads come from different gems
func NotWhitelist ¶
func NotWhitelist(a *FastQRecord) bool
func SliceCompare ¶
* A utility function to compare two slices
Types ¶
type FastQReader ¶
type FastQReader struct {
Source *ZipReader
Buffer *bufio.Reader
Line int
DefferedError error
Pending *FastQRecord
LastBarcode []byte
}
* This struture reprensets a "fastQ" reader that can pull single records * as well as sets of records (on the same barcode) from a fastq file
func (*FastQReader) ReadBarcodeSet ¶
func (fqr *FastQReader) ReadBarcodeSet(space *[]FastQRecord, trim int) ([]FastQRecord, error, bool)
* Reaturn an array of all of the reads from the same GEM. * "space" may be null or may be the result of a previous call to this function. * If present the array will be destructively re-used
func (*FastQReader) ReadOneLine ¶
func (fqr *FastQReader) ReadOneLine(result *FastQRecord, trim int) error
* Read a single record from a fastQ file
type FastQRecord ¶
type FastQRecord struct {
Read1 []byte
ReadQual1 []byte
Read2 []byte
ReadQual2 []byte
TrimBases []byte
TrimQuals []byte
Barcode10X []byte
Barcode10XQual []byte
RawBarcode10X []byte
Barcode []byte
BarcodeQual []byte
ReadInfo string
ReadGroupId string
}
* This structure represents a single read from a fastq file
type ZipReader ¶
type ZipReader struct {
/* The exact reader that was passed to us */
Source io.Reader
Cmd *exec.Cmd
}
* We need a "ZipReader" reader object. A ZipReader contains a source reader * but implements a read function that retries if the source reader returned * fewer bytes than requested.
func FastZipReader ¶
* Implement an "uncompressing" reader that uses the system's * gunzip program to uncompress the input file. We do this * because the system gzip is much much faster than the go library
Source Files