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複数のcstagのconsensusを作る関数

Example

import cstag
cs_list = ["cs:Z:=ACGT", "cs:Z:=AC*gt*T", "cs:Z:=AC*gt*T"]
cstag.consensus(cs_list)
# cs:Z:=AC*gt*T

Output a html report from cs tag

• insertion = red
• deletion = skyblue
• substitution = green

For the JoSS review at openjournals/joss-reviews/issues/6066.

The CS (uppercase) is a reserved for color read sequence information as per the SAM format, while the cs (lowercase)
tag represents the difference string. This has already been a topic of discussion while feature requests to incorporate the cs tag more
formally into the SAM format.

It might be beneficial to change the "CS" to "cs" in all documentation so as to not mislead users.

Not sure if this is feasible to implement, but I wanted to make this request which would make cstag more useful to our group.

Right now the consensus function doesn't contain any mechanism for checking the "quality" of the consensus. In our work, we often want to try to call a consensus, but also be able to discard sets of reads if the consensus isn't in good agreement. This is common in sequencing of amplicons for many purposes. Eg, we would ideally like:

1. Return the consensus if the individual cs tags agree at at least some level that could be different from majority voting. (eg, maybe we say 75% have to agree). If they don't, provide some indication consensus should be dropped.
2. Similarly be able to report the maximal edit distance of any one tag from the others.

samファイルからcstagを呼び出す関数 calcsの移植

Args:

• list of multiple cs tags
• clustering methods

Return:

• Index of the cluster each sample belongs to.

cs tagをMIDSに変換する関数

Mask nucleotide with low phred score into N.

For the JoSS review at openjournals/joss-reviews/issues/6066

Please see https://github.com/betteridiot/joss_reviews/blob/master/cstag/joss_review.md for complete notes.

Doctests for cstag do not pass due to minor syntax errors. See Testing doctests. As doctests should also be testable (given their nature), this should be addressed.