So are these two gaprc values deprecated in the new 1.6.0 version of the staden pkg release? I was using these settings to drop columns that were partially padded. And our finishers have gotten used to using this feature. They all have CONTIG_EDITOR.SHUFFLE_PADS.CONSENSUS_CUTOFF .75 in their .gaprc files.
Seems the new version of shuffle pads in 1.6.0 only drops full columns of pads (100%). Is there some other way to still do what the older version of shuffle pads did?
# Modifying these will control when shuffle pads thinks an "entire column of
# pads" really is one. This allows it to be fooled into deleted columns that
# are almost pads. It's definition is - calculate the consensus and if it's a
# pad then it's an entire column. The consensus_mode 0 (frequency) and cutoff
# 1 (100%) are the defaults, which therefore really do mean entirely pads.
set_def CONTIG_EDITOR.SHUFFLE_PADS.CONSENSUS_MODE 0
set_def CONTIG_EDITOR.SHUFFLE_PADS.CONSENSUS_CUTOFF 1
Indeed the replacement does not have this feature any more.
However it turned out that rather a lot of people liked the contig editor shuffle pads feature purely for its "column-of-pads removal" code, despite having general universal distaste for the rather poor realignment ability.
This wasn't something I'd realised before hand, but most recently I added it back as "Strip Pads" within the editor. This new version does no pad movement at all - it's purely for removing columns of pads. Due to the name change the new settings were also changed:
set_def CONTIG_EDITOR.STRIP_PADS.CONSENSUS_MODE 0
set_def CONTIG_EDITOR.STRIP_PADS.CONSENSUS_CUTOFF 1
It's not in 1.6.0 though yet, although if you're brave it is in the CVS tree (src/gap4/edCommands.c would be a starting point).
I plan on releasing 1.6.1 as a bug fix to 1.6.0 soon (for possibly long periods of "soon" if past history is anything to go by though) as there's a few other issues to sort out.