Update generate_permit_list.rst

`--unfiltered-pl` is no longer beta.

docs/source/generate_permit_list.rst

@@ -33,7 +33,7 @@ barcodes are decided):
   a number of reads >= to the <ncells>-th barcode will be considered part of the permit list, all others will not 
   (but will be considered for correction to this permit list).
 
-* ``--valid-bc <bcfile>``: This option will read the provided file <bcfile> and treat it as an explicitly-provided list of true, filtered barcodes (i.e. a list of barcodes believed to belong to a set of high-confidence cells truly present in the given sample). Barcodes appearing in this list will be considered to correspond to true and filtered cells, and barcodes will be corrected to this list. This flag is *not* designed to perform unfiltered quantification (i.e. correcting to a list of all *possible* barcodes generated by a technology, like e.g. the `10x v3 permit list <https://raw.githubusercontent.com/10XGenomics/cellranger/master/lib/python/cellranger/barcodes/translation/3M-february-2018.txt.gz>`_).  To correct against an *unfiltered* permit list, you should use the ``--unfiltered-pl`` flag described below (which is currently in beta).
+* ``--valid-bc <bcfile>``: This option will read the provided file <bcfile> and treat it as an explicitly-provided list of true, filtered barcodes (i.e. a list of barcodes believed to belong to a set of high-confidence cells truly present in the given sample). Barcodes appearing in this list will be considered to correspond to true and filtered cells, and barcodes will be corrected to this list. This flag is *not* designed to perform unfiltered quantification (i.e. correcting to a list of all *possible* barcodes generated by a technology, like e.g. the `10x v3 permit list <https://raw.githubusercontent.com/10XGenomics/cellranger/master/lib/python/cellranger/barcodes/translation/3M-february-2018.txt.gz>`_).  To correct against an *unfiltered* permit list, you should use the ``--unfiltered-pl`` flag described below.
 
 * ``--unfiltered-pl <plist>``: This option accepts as an argument a list of *possible* barcodes for the sample.  For example, this is the flag you should use if you wish to provide an "external permit list", like the 10x v2 or 10x v3 permit lists. Unilike with the ``--valid-bc`` flag, the list passed to this argument is the set of all possible barcodes for the technology being processed, and it is likely that most of the barcodes in the file may not correspond to cells present in this particular sample.  When using this argument, you may also pass the ``--min-reads`` argument to determine the minimum frequency with which a barcode must be seen in order to be retained.  The algorithm used here will pass over the input records (mapped reads) and count how many times each of the barcodes in the unfiltered permit list occur exactly.  Any barcode ocurring >= ``min-reads`` times will be considered as a present cell.  Subsequently, all barcodes that did not match a present cell will be searched (at an edit distance of up to 1) againt the barcodes determined to correspond to present cells.  If an initially non-matching barcode has a unique neighbor among the barcodes for present cells, it will be corrected to that barcode, but if it has no 1-edit neighbor, or if it has 2 or more 1-edit neighbors among that list (i.e. it's correction would be ambiguous), then the record is discarded.