"""
Coverage datatypes
"""
import logging
import math
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.tabular import Tabular
log = logging.getLogger(__name__)
[docs]class LastzCoverage(Tabular):
file_ext = "coverage"
MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)
MetadataElement(name="positionCol", default=2, desc="Position column", param=metadata.ColumnParameter)
MetadataElement(
name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter
)
MetadataElement(
name="reverseCol",
desc="Optional reverse read column",
param=metadata.ColumnParameter,
optional=True,
no_value=0,
)
MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
[docs] def get_track_resolution(self, dataset, start, end):
range = end - start
# Determine appropriate resolution to plot ~1000 points
resolution = math.ceil(10 ** math.ceil(math.log10(range / 1000)))
# Restrict to valid range
resolution = min(resolution, 10000)
resolution = max(resolution, 1)
return resolution