Refactoring codes for removing buffer size options. An some other changes...

Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce

doc/book/annexes.qmd

@@ -1,82 +1,107 @@
 # Annexes
 
-### Sequence attributes
+## Sequence attributes
 
-#### Reserved sequence attributes
+**ali_dir (`string`)**
 
-##### `ali_dir`
+  - Set by the *obipairing* tool
+  - The attribute can contain 2 string values `left` or `right`.
 
-###### Type : `string`
+  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*.
 
-The attribute can contain 2 string values `"left"` or `"right".`
+**ali_length (`int`)**
 
-###### Set by the *obipairing* tool
+  - 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*.
+  Length of the aligned parts when merging forward and reverse reads
 
-##### `ali_length`
 
-###### Set by the *obipairing* tool
+**count (`int`)**
 
-Length of the aligned parts when merging forward and reverse reads
+  - Set by the *obiuniq* tool
+  - Getter : method `Count()`
+  - Setter : method `SetCount(int)`
 
-##### `count` : the number of sequence occurrences
+  The `count` attribute indicates how-many strictly identical reads
+  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.
 
-###### Set by the *obiuniq* tool
+  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
 
-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.
+**merged_* (`map[string]int`)**
 
-###### Getter : method `Count()`
+  - Set by the *obiuniq* tool
 
-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
+  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*.
 
-##### `merged_*`
+**mode (`string`)**
 
-###### Type : `map[string]int`
+  - Set by the *obipairing* tool
+  - The attribute can contain 2 string values `join` or `alignment`.
 
-###### 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*.
+**obitag_ref_index (`map[string]string`)**
 
-##### `mode`
+  - Set by the *obirefidx* tool.
 
-###### Set by the *obipairing* 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. 
 
-**`obitag_ref_index`**
+```json
+   {"0":"9606@Homo sapiens@species",
+    "2":"207598@Homininae@subfamily",
+    "3":"9604@Hominidae@family",
+    "8":"314295@Hominoidea@superfamily",
+    "10":"9526@Catarrhini@parvorder",
+    "12":"1437010@Boreoeutheria@clade",
+    "16":"9347@Eutheria@clade",
+    "17":"40674@Mammalia@class",
+    "22":"117571@Euteleostomi@clade",
+    "25":"7776@Gnathostomata@clade",
+    "29":"33213@Bilateria@clade",
+    "30":"6072@Eumetazoa@clade"}
+```
 
-###### Set by the *obirefidx* tool.
+**pairing_mismatches (`map[string]string`)**
 
-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.
+  - Set by the *obipairing* tool
 
-###### Getter : method `Count()`
+**seq_a_single (`int`)**
 
-##### `pairing_mismatches`
+  - Set by the *obipairing* tool
 
-###### Set by the *obipairing* tool
+**seq_ab_match (`int`)**
 
-##### `score`
+  - Set by the *obipairing* tool
 
-###### Set by the *obipairing* tool
+**seq_b_single (`int`)**
 
-##### `score_norm`
+  - Set by the *obipairing* tool
 
-###### Set by the *obipairing* tool
+**score (`int`)**
+
+  - Set by the *obipairing* tool
+
+**score_norm (`float`)**
+
+  - Set by the *obipairing* tool
+  - The value ranges between 0 and 1.
+
+  Score of the alignment between forward and reverse reads expressed as a fraction of identity.
+