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Merge branch 'release/1.3.1'
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  -Support for version 3 GTC files during locus aggregation
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Kelley, Ryan committed Nov 16, 2017
2 parents ff95f6e + 0cfb2b4 commit 654389e
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3 changes: 3 additions & 0 deletions change_log.txt
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@@ -1,3 +1,6 @@
1.3.1
-Support for version 3 GTC files during locus aggregation

1.3.0
-Added new function to assist with aggregation of information across samples for loci (see LocusAggregate)
-Added new class to parse binary EGT files
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7 changes: 4 additions & 3 deletions module/LocusAggregate.py
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Expand Up @@ -24,7 +24,8 @@ def __init__(self, locus_offset, loci_buffer_size, normalization_lookups):
def __call__(self, sample_data):
"""
Based on the configuration of the Loader function, load a slice of loci data
from the given sample.
from the given sample. If the sample data is not version 4 or above, the log_r_ratios
and b_allele_freqs will be populated with an array of "None"
Args:
sample_data (GenotypeCalls): The sample data to provide loci information
Expand All @@ -40,9 +41,9 @@ def __call__(self, sample_data):
locus_aggregate.scores = sample_data.get_genotype_scores(
locus_offset, loci_buffer_size)
locus_aggregate.b_allele_freqs = sample_data.get_ballele_freqs(
locus_offset, loci_buffer_size)
locus_offset, loci_buffer_size) if sample_data.version >= 4 else [None] * loci_buffer_size
locus_aggregate.log_r_ratios = sample_data.get_logr_ratios(
locus_offset, loci_buffer_size)
locus_offset, loci_buffer_size) if sample_data.version >= 4 else [None] * loci_buffer_size
locus_aggregate.x_intensities = sample_data.get_raw_x_intensities(
locus_offset, loci_buffer_size)
locus_aggregate.y_intensities = sample_data.get_raw_y_intensities(
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2 changes: 1 addition & 1 deletion module/__init__.py
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Expand Up @@ -25,7 +25,7 @@
# of the authors and should not be interpreted as representing official policies,
# either expressed or implied, of the FreeBSD Project.

__version__ = "1.3.0"
__version__ = "1.3.1"
from .GenotypeCalls import code2genotype, NC, AA, AB, BB, GenotypeCalls, NormalizationTransform, ScannerData
from .BeadPoolManifest import RefStrand, SourceStrand, BeadPoolManifest
from .LocusAggregate import LocusAggregate
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