5 Annexes
5.0.1 Sequence attributes
5.0.1.1 Reserved sequence attributes
5.0.1.1.1 ali_dir
5.0.1.1.1.1 Type : string
The attribute can contain 2 string values "left" or "right".
5.0.1.1.1.2 Set by the obipairing tool
The alignment generated by obipairing is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction ali_dir is set to left. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, ali_dir is set to right.
5.0.1.1.2 ali_length
5.0.1.1.2.1 Set by the obipairing tool
Length of the aligned parts when merging forward and reverse reads
5.0.1.1.3 count : the number of sequence occurrences
5.0.1.1.3.1 Set by the obiuniq tool
The count attribute indicates how-many strictly identical sequences have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.
5.0.1.1.3.2 Getter : method Count()
The Count() method allows to access to the count attribute as an integer value. If the count attribute is not defined for the given sequence, the value 1 is returned
5.0.1.1.4 merged_*
5.0.1.1.4.1 Type : map[string]int
5.0.1.1.4.2 Set by the obiuniq tool
The -m option of the obiuniq tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when obiuniq is run after running obimultiplex. The actual name of the attribute depends on the name of the monitored attribute. If -m option is used with the attribute sample, then this attribute names merged_sample.
5.0.1.1.5 mode
5.0.1.1.5.1 Set by the obipairing tool
obitag_ref_index
5.0.1.1.5.2 Set by the obirefidx tool.
It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.