Opened 8 years ago

Closed 7 years ago

#775 closed request (fixed)

uncompressed OutBamFile

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.12
Component: omic Version:
Keywords: Cc:

Description

In libbam one can set the compression level, and e.g. 'u' in mode encodes for uncompressed output. This is useful especially when piping to to another program and it is desirable to avoid compression/decompression.

Change History (3)

comment:1 Changed 7 years ago by Peter

samtools accepts a char (as third letter in mode string) that decides the compression level. This char must either be a digit - '9'? or 'u' where the latter is an alias for '0'. I believe default is 6 but that is probably depending on libz and might be configurable (who knows). We currently have a constructor

OutBamFile(string, BamHeader)

I suggest we add another constructor taking a third argument (and an equivalent open function). This third argument should either be unsigned int or a char. For the former we require that the number is in range [0-9] (otherwise throw) and translate it to correct char so we can inject into mode[2]. If we prefer char in our interface, we can just copy the char directory into mode (after checking validity, of course).

comment:2 Changed 7 years ago by Peter

Status: newassigned

comment:3 Changed 7 years ago by Peter

Resolution: fixed
Status: assignedclosed

(In [3160]) closes #775

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