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