--split-sequences specifies number of GMTK frames and not number of base pairs

[EricR86]

Original report (BitBucket issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

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Currently in the --help, --split-sequences is defined as follows:

    -S SIZE, --split-sequences=SIZE
                        split up sequences that are larger than SIZE bp
                        (default 2000000)

Where "bp" stands for "base pair". However currently in the code --split-sequences clearly specifies the number of GMTK frames instead which are not equivalent for cases where the resolution is larger than 1:

In segway/run.py line 656 where the options are copied over to python attributes:

                        ("split_sequences", "max_frames"),

and in segway/run.py line 1231:

        directives["CARD_FRAMEINDEX"] = self.max_frames

[EricR86]

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

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I should also note that the default for --split-sequences is defined by MAX_FRAMES:

        group.add_option("-S", "--split-sequences", metavar="SIZE",
                         default=MAX_FRAMES, type=int,
                         help="split up sequences that are larger than SIZE "
                         "bp (default %s)" % MAX_FRAMES)

[EricR86]

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

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• changed state from "new" to "resolved"

Fixed in pull request #44