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doc/04_OBITools_doc.Rmd

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+# Annexes
+
+### Sequence attributes
+
+#### Reserved sequence attributes
+
+##### `ali_dir`
+
+###### Type : `string`
+
+The attribute can contain 2 string values `"left"` or `"right".`
+
+###### 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*.
+
+##### `ali_length`
+
+###### Set by the *obipairing* tool
+
+Length of the aligned parts when merging forward and reverse reads
+
+##### `count` : the number of sequence occurrences
+
+###### 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.
+
+###### 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
+
+##### `merged_*`
+
+###### Type : `map[string]int`
+
+###### 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*.
+
+##### `mode`
+
+###### Set by the *obipairing* tool
+
+**`obitag_ref_index`**
+
+###### 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.
+
+###### Getter : method `Count()`
+
+##### `pairing_mismatches`
+
+###### Set by the *obipairing* tool
+
+##### `score`
+
+###### Set by the *obipairing* tool
+
+##### `score_norm`
+
+###### Set by the *obipairing* tool