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sctools package
sctools.metrics package
sctools.test package
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Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
_
__init__() (sctools.metrics.gatherer.GatherCellMetrics method)
(sctools.metrics.gatherer.GatherGeneMetrics method)
(sctools.metrics.gatherer.MetricGatherer method)
__iter__() (sctools.gtf.Reader method)
A
AlignmentSortOrder (class in sctools.bam)
antisense_reads (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
args (sctools.bam.SortError attribute)
attach_barcodes() (sctools.platform.BarcodePlatform class method)
(sctools.platform.BarcodePlatform method)
(sctools.platform.TenXV2 class method)
(sctools.platform.TenXV2 method)
average_quality() (sctools.fastq.Record method)
,
[1]
(sctools.fastq.StrRecord method)
,
[1]
B
bam_file (sctools.metrics.gatherer.GatherCellMetrics property)
(sctools.metrics.gatherer.GatherGeneMetrics property)
(sctools.metrics.gatherer.MetricGatherer property)
bam_to_count_matrix() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
bamfile() (in module sctools.test.test_bam)
barcode_generator_with_corrected_cell_barcodes() (in module sctools.test.test_fastq)
barcode_set() (in module sctools.test.test_barcode)
BarcodeGeneratorWithCorrectedCellBarcodes (class in sctools.fastq)
BarcodePlatform (class in sctools.platform)
Barcodes (class in sctools.barcode)
base4_entropy() (in module sctools)
(in module sctools.stats)
base_frequency() (sctools.barcode.Barcodes method)
bits_per_base (sctools.encodings.Encoding attribute)
,
[1]
(sctools.encodings.ThreeBit attribute)
,
[1]
(sctools.encodings.TwoBit attribute)
,
[1]
bytes_fastq_record() (in module sctools.test.test_fastq)
C
calculate_cell_metrics() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
calculate_gene_metrics() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
calculate_variance() (sctools.stats.OnlineGaussianSufficientStatistic method)
,
[1]
cell_barcode (sctools.platform.BarcodePlatform attribute)
,
[1]
(sctools.platform.TenXV2 attribute)
,
[1]
cell_barcode_fraction_bases_above_30_mean (sctools.metrics.aggregator.CellMetrics attribute)
cell_barcode_fraction_bases_above_30_variance (sctools.metrics.aggregator.CellMetrics attribute)
CellMetrics (class in sctools.metrics.aggregator)
chromosome (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
Classes() (in module sctools)
,
[1]
,
[2]
,
[3]
close() (sctools.metrics.writer.MetricCSVWriter method)
,
[1]
correct_bam() (sctools.barcode.ErrorsToCorrectBarcodesMap method)
,
[1]
D
decode() (sctools.encodings.Encoding method)
,
[1]
(sctools.encodings.ThreeBit class method)
(sctools.encodings.ThreeBit method)
(sctools.encodings.TwoBit method)
,
[1]
decoding_map (sctools.encodings.Encoding attribute)
,
[1]
(sctools.encodings.ThreeBit attribute)
,
[1]
(sctools.encodings.TwoBit attribute)
,
[1]
duplicate_reads (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
E
effective_diversity() (sctools.barcode.Barcodes method)
embedded_barcode_generator() (in module sctools.test.test_fastq)
EmbeddedBarcode (in module sctools.fastq)
EmbeddedBarcodeGenerator (class in sctools.fastq)
encode() (sctools.encodings.Encoding class method)
(sctools.encodings.Encoding method)
(sctools.encodings.ThreeBit class method)
(sctools.encodings.ThreeBit method)
(sctools.encodings.TwoBit class method)
(sctools.encodings.TwoBit method)
encoder() (in module sctools.test.test_encodings)
encoder_2bit() (in module sctools.test.test_encodings)
encoder_3bit() (in module sctools.test.test_encodings)
Encoding (class in sctools.encodings)
encoding_map (sctools.encodings.Encoding attribute)
,
[1]
(sctools.encodings.ThreeBit attribute)
,
[1]
(sctools.encodings.TwoBit attribute)
,
[1]
end (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
ErrorsToCorrectBarcodesMap (class in sctools.barcode)
execute() (sctools.metrics.merge.MergeCellMetrics method)
(sctools.metrics.merge.MergeGeneMetrics method)
(sctools.metrics.merge.MergeMetrics method)
,
[1]
extra_docs (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.gatherer.GatherCellMetrics attribute)
(sctools.metrics.gatherer.GatherGeneMetrics attribute)
extract_barcode() (in module sctools)
(in module sctools.fastq)
extract_cell_barcode() (sctools.fastq.BarcodeGeneratorWithCorrectedCellBarcodes method)
,
[1]
extract_extended_gene_names() (in module sctools.gtf)
extract_gene_exons() (in module sctools.gtf)
extract_gene_names() (in module sctools.gtf)
extract_metrics() (sctools.metrics.gatherer.GatherCellMetrics method)
(sctools.metrics.gatherer.GatherGeneMetrics method)
(sctools.metrics.gatherer.MetricGatherer method)
,
[1]
,
[2]
F
feature (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
filename (sctools.metrics.writer.MetricCSVWriter property)
filenames (sctools.fastq.BarcodeGeneratorWithCorrectedCellBarcodes property)
(sctools.fastq.EmbeddedBarcodeGenerator property)
(sctools.fastq.Reader property)
(sctools.gtf.Reader property)
(sctools.reader.Reader property)
files() (in module sctools.test.test_gtf)
filter() (sctools.gtf.Reader method)
,
[1]
finalize() (sctools.metrics.aggregator.CellMetrics method)
,
[1]
(sctools.metrics.aggregator.GeneMetrics method)
,
[1]
(sctools.metrics.aggregator.MetricAggregator method)
,
[1]
fragments_per_molecule (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
fragments_with_single_read_evidence (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
frame (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
from_aligned_segment() (sctools.bam.TagSortableRecord class method)
from_iterable_bytes() (sctools.barcode.Barcodes class method)
from_iterable_encoded() (sctools.barcode.Barcodes class method)
from_iterable_strings() (sctools.barcode.Barcodes class method)
from_whitelist() (sctools.barcode.Barcodes class method)
G
GatherCellMetrics (class in sctools.metrics.gatherer)
,
[1]
GatherGeneMetrics (class in sctools.metrics.gatherer)
,
[1]
gc_content() (sctools.encodings.Encoding method)
,
[1]
(sctools.encodings.ThreeBit class method)
(sctools.encodings.ThreeBit method)
(sctools.encodings.TwoBit method)
,
[1]
GeneMetrics (class in sctools.metrics.aggregator)
GenericPlatform (class in sctools.platform)
genes_detected_multiple_observations (sctools.metrics.aggregator.CellMetrics attribute)
genomic_read_quality_mean (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
genomic_read_quality_variance (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
genomic_reads_fraction_bases_quality_above_30_mean (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
genomic_reads_fraction_bases_quality_above_30_variance (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
get_attribute() (sctools.gtf.GTFRecord method)
,
[1]
get_barcode_for_alignment() (in module sctools.bam)
get_barcodes_from_bam() (in module sctools.bam)
get_corrected_barcode() (sctools.barcode.ErrorsToCorrectBarcodesMap method)
,
[1]
get_mitochondrial_gene_names() (in module sctools.gtf)
get_sort_key() (sctools.bam.QueryNameSortOrder static method)
get_tag_or_default() (in module sctools.bam)
get_tags() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
group_qc_outputs() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
GTFRecord (class in sctools.gtf)
H
hamming_distance() (sctools.encodings.Encoding method)
(sctools.encodings.Encoding static method)
(sctools.encodings.ThreeBit method)
(sctools.encodings.ThreeBit static method)
(sctools.encodings.TwoBit method)
(sctools.encodings.TwoBit static method)
I
i7_files_compressions_and_modes() (in module sctools.test.test_fastq)
indices() (in module sctools.test.test_bam)
indices_by_chromosome() (sctools.bam.SubsetAlignments method)
,
[1]
infer_open() (in module sctools)
(in module sctools.reader)
iter_cell_barcodes() (in module sctools.bam)
iter_genes() (in module sctools.bam)
iter_molecule_barcodes() (in module sctools.bam)
iter_tag_groups() (in module sctools.bam)
iupac_ambiguous (sctools.encodings.TwoBit.TwoBitEncodingMap attribute)
K
key_generator (sctools.bam.AlignmentSortOrder property)
(sctools.bam.QueryNameSortOrder property)
M
make_records_from_values() (in module sctools.test.test_bam)
map_ (sctools.encodings.ThreeBit.ThreeBitEncodingMap attribute)
(sctools.encodings.TwoBit.TwoBitEncodingMap attribute)
mean (sctools.stats.OnlineGaussianSufficientStatistic property)
mean() (sctools.stats.OnlineGaussianSufficientStatistic method)
mean_and_variance() (sctools.stats.OnlineGaussianSufficientStatistic method)
,
[1]
merge_bams() (in module sctools.bam)
merge_cell_metrics() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
merge_count_matrices() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
merge_gene_metrics() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
mergeable_cell_metrics() (in module sctools.test.test_metrics)
mergeable_gene_metrics() (in module sctools.test.test_metrics)
MergeCellMetrics (class in sctools.metrics.merge)
MergeGeneMetrics (class in sctools.metrics.merge)
MergeMetrics (class in sctools.metrics.merge)
MetricAggregator (class in sctools.metrics.aggregator)
MetricCSVWriter (class in sctools.metrics.writer)
MetricGatherer (class in sctools.metrics.gatherer)
,
[1]
module
sctools.bam
sctools.barcode
sctools.encodings
sctools.fastq
sctools.gtf
sctools.metrics.aggregator
sctools.metrics.gatherer
sctools.metrics.merge
sctools.metrics.writer
sctools.platform
sctools.reader
sctools.stats
sctools.test.test_bam
sctools.test.test_barcode
sctools.test.test_encodings
sctools.test.test_entrypoints
sctools.test.test_fastq
sctools.test.test_gtf
sctools.test.test_metrics
sctools.test.test_stats
molecule_barcode (sctools.platform.BarcodePlatform attribute)
,
[1]
(sctools.platform.TenXV2 attribute)
,
[1]
molecule_barcode_fraction_bases_above_30_mean (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
molecule_barcode_fraction_bases_above_30_variance (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
molecules_with_single_read_evidence (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
N
n_fragments (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
n_genes (sctools.metrics.aggregator.CellMetrics attribute)
n_mitochondrial_genes (sctools.metrics.aggregator.CellMetrics attribute)
n_mitochondrial_molecules (sctools.metrics.aggregator.CellMetrics attribute)
n_molecules (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
n_nonspecific() (in module sctools.test.test_bam)
n_reads (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
n_specific() (in module sctools.test.test_bam)
name (sctools.fastq.Record attribute)
(sctools.fastq.Record property)
(sctools.fastq.StrRecord attribute)
(sctools.fastq.StrRecord property)
name2 (sctools.fastq.Record attribute)
(sctools.fastq.Record property)
(sctools.fastq.StrRecord attribute)
(sctools.fastq.StrRecord property)
noise_reads (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
number_cells_detected_multiple (sctools.metrics.aggregator.GeneMetrics attribute)
number_cells_expressing (sctools.metrics.aggregator.GeneMetrics attribute)
O
OnlineGaussianSufficientStatistic (class in sctools.stats)
P
parse_extra_fields() (sctools.metrics.aggregator.CellMetrics method)
(sctools.metrics.aggregator.GeneMetrics method)
(sctools.metrics.aggregator.MetricAggregator method)
parse_molecule() (sctools.metrics.aggregator.CellMetrics method)
,
[1]
(sctools.metrics.aggregator.GeneMetrics method)
,
[1]
(sctools.metrics.aggregator.MetricAggregator method)
,
[1]
pct_mitochondrial_molecules (sctools.metrics.aggregator.CellMetrics attribute)
perfect_cell_barcodes (sctools.metrics.aggregator.CellMetrics attribute)
perfect_molecule_barcodes (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
Q
quality (sctools.fastq.Record attribute)
(sctools.fastq.Record property)
(sctools.fastq.StrRecord attribute)
(sctools.fastq.StrRecord property)
QueryNameSortOrder (class in sctools.bam)
R
Reader (class in sctools.fastq)
(class in sctools.gtf)
(class in sctools.reader)
reader_all_compressions() (in module sctools.test.test_fastq)
reads_mapped_exonic (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_mapped_intergenic (sctools.metrics.aggregator.CellMetrics attribute)
reads_mapped_intronic (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_mapped_multiple (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_mapped_too_many_loci (sctools.metrics.aggregator.CellMetrics attribute)
reads_mapped_uniquely (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_mapped_utr (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_per_fragment (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
reads_per_molecule (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
Record (class in sctools.fastq)
S
sa_object() (in module sctools.test.test_bam)
sample_barcode (sctools.platform.BarcodePlatform attribute)
,
[1]
(sctools.platform.TenXV2 attribute)
,
[1]
score (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
sctools.bam
module
sctools.barcode
module
sctools.encodings
module
sctools.fastq
module
sctools.gtf
module
sctools.metrics.aggregator
module
sctools.metrics.gatherer
module
sctools.metrics.merge
module
sctools.metrics.writer
module
sctools.platform
module
sctools.reader
module
sctools.stats
module
sctools.test.test_bam
module
sctools.test.test_barcode
module
sctools.test.test_encodings
module
sctools.test.test_entrypoints
module
sctools.test.test_fastq
module
sctools.test.test_gtf
module
sctools.test.test_metrics
module
sctools.test.test_stats
module
select_record_indices() (sctools.fastq.BarcodeGeneratorWithCorrectedCellBarcodes method)
(sctools.fastq.EmbeddedBarcodeGenerator method)
(sctools.fastq.Reader method)
(sctools.gtf.Reader method)
(sctools.reader.Reader method)
seqname (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
sequence (sctools.fastq.Record attribute)
(sctools.fastq.Record property)
(sctools.fastq.StrRecord attribute)
(sctools.fastq.StrRecord property)
sequence() (in module sctools.test.test_encodings)
set_attribute() (sctools.gtf.GTFRecord method)
,
[1]
short_barcode_set_from_encoded() (in module sctools.test.test_barcode)
short_barcode_set_from_iterable() (in module sctools.test.test_barcode)
simple_barcodes() (in module sctools.test.test_encodings)
simple_hamming_distances() (in module sctools.test.test_encodings)
single_hamming_errors_from_whitelist() (sctools.barcode.ErrorsToCorrectBarcodesMap class method)
size (sctools.fastq.BarcodeGeneratorWithCorrectedCellBarcodes property)
(sctools.fastq.EmbeddedBarcodeGenerator property)
(sctools.fastq.Reader property)
(sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
(sctools.gtf.Reader property)
(sctools.reader.Reader property)
sort_by_tags_and_queryname() (in module sctools.bam)
SortError
source (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
spliced_reads (sctools.metrics.aggregator.CellMetrics attribute)
(sctools.metrics.aggregator.GeneMetrics attribute)
(sctools.metrics.aggregator.MetricAggregator attribute)
split() (in module sctools.bam)
split_bam() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
split_metrics_file() (in module sctools.test.test_metrics)
start (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
strand (sctools.gtf.GTFRecord attribute)
(sctools.gtf.GTFRecord property)
string_fastq_record() (in module sctools.test.test_fastq)
StrRecord (class in sctools.fastq)
SubsetAlignments (class in sctools.bam)
summarize_hamming_distances() (sctools.barcode.Barcodes method)
T
tag() (sctools.bam.Tagger method)
,
[1]
tag_sort_bam() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
tagged_bam() (in module sctools.test.test_bam)
tagged_bamfile() (in module sctools.test.test_barcode)
Tagger (class in sctools.bam)
TagSortableRecord (class in sctools.bam)
TenXV2 (class in sctools.platform)
test_Attach10XBarcodes_entrypoint() (in module sctools.test.test_entrypoints)
test_Attach10XBarcodes_entrypoint_with_whitelist() (in module sctools.test.test_entrypoints)
test_AttachBarcodes_entrypoint_with_whitelist() (in module sctools.test.test_entrypoints)
test_balanced_data_produces_entropy_1() (in module sctools.test.test_stats)
test_balanced_unnormalized_data_produces_entropy_1() (in module sctools.test.test_stats)
test_barcode_diversity_is_in_range() (in module sctools.test.test_barcode)
test_base_frequency_sums_are_all_equal_to_barcode_set_length() (in module sctools.test.test_barcode)
test_bytes_fastq_record_quality_score_parsing() (in module sctools.test.test_fastq)
test_calculate_cell_metrics_cli() (in module sctools.test.test_metrics)
test_calculate_gene_metrics_cli() (in module sctools.test.test_metrics)
test_cell_metrics_mean_n_genes_observed() (in module sctools.test.test_metrics)
test_chromosome_19_comes_before_21() (in module sctools.test.test_bam)
test_concentrated_data_produces_entropy_0() (in module sctools.test.test_stats)
test_concentrated_unnormalized_data_produces_entropy_0() (in module sctools.test.test_stats)
test_correct_bam_produces_cb_tags() (in module sctools.test.test_barcode)
test_correct_barcode_finds_and_corrects_1_base_errors() (in module sctools.test.test_barcode)
test_correct_barcode_raises_keyerror_when_barcode_has_more_than_one_error() (in module sctools.test.test_barcode)
test_correct_barcode_raises_keyerror_when_barcode_not_correct_length() (in module sctools.test.test_barcode)
test_correct_number_of_indices_are_extracted() (in module sctools.test.test_bam)
test_corrects_barcodes() (in module sctools.test.test_fastq)
test_count_merge() (in module sctools.test.test_entrypoints)
test_duplicate_records() (in module sctools.test.test_metrics)
test_embedded_barcode_generator_produces_outputs_of_expected_size() (in module sctools.test.test_fastq)
test_encoded_hamming_distance_is_accurate() (in module sctools.test.test_encodings)
test_fastq_returns_correct_filesize_for_single_and_multiple_files() (in module sctools.test.test_fastq)
test_fields_populate_properly() (in module sctools.test.test_fastq)
test_fragments_number_is_greater_than_molecule_number() (in module sctools.test.test_metrics)
test_gene_metrics_n_genes() (in module sctools.test.test_metrics)
test_get_barcode_for_alignment() (in module sctools.test.test_bam)
test_get_barcode_for_alignment_raises_error_for_missing_tag() (in module sctools.test.test_bam)
test_get_barcodes_from_bam() (in module sctools.test.test_bam)
test_get_barcodes_from_bam_with_raise_missing_true_raises_warning_without_cr_barcode_passed() (in module sctools.test.test_bam)
test_gzip_compression() (in module sctools.test.test_metrics)
test_higher_order_metrics_by_gene() (in module sctools.test.test_metrics)
test_incorrect_extension_does_not_raise_when_open_mode_is_specified() (in module sctools.test.test_bam)
test_incorrect_extension_without_open_mode_raises_value_error() (in module sctools.test.test_bam)
test_incorrect_input_raises_errors() (in module sctools.test.test_barcode)
test_indices_are_all_greater_than_zero() (in module sctools.test.test_bam)
test_invalid_open_mode_raises_valueerror() (in module sctools.test.test_fastq)
test_iterable_produces_correct_barcodes() (in module sctools.test.test_barcode)
test_merge_cell_metrics_cli() (in module sctools.test.test_metrics)
test_merge_cell_metrics_does_not_correct_duplicates() (in module sctools.test.test_metrics)
test_merge_gene_metrics_averages_over_multiply_detected_genes() (in module sctools.test.test_metrics)
test_merge_gene_metrics_cli() (in module sctools.test.test_metrics)
test_metrics_highest_expression_class() (in module sctools.test.test_metrics)
test_metrics_highest_read_count() (in module sctools.test.test_metrics)
test_metrics_n_fragments() (in module sctools.test.test_metrics)
test_metrics_n_molecules() (in module sctools.test.test_metrics)
test_metrics_n_reads() (in module sctools.test.test_metrics)
test_metrics_number_perfect_cell_barcodes() (in module sctools.test.test_metrics)
test_metrics_number_perfect_molecule_barcodes() (in module sctools.test.test_metrics)
test_mixed_filetype_read_gets_correct_record_number() (in module sctools.test.test_fastq)
test_non_string_filename_in_iterable_raises_typeerror() (in module sctools.test.test_fastq)
test_non_string_filename_raises_typeerror() (in module sctools.test.test_fastq)
test_opens_file_parses_size() (in module sctools.test.test_gtf)
test_opens_file_populates_fields_properly() (in module sctools.test.test_gtf)
test_opens_file_reads_first_line() (in module sctools.test.test_gtf)
test_printing_bytes_record_generates_valid_fastq_record() (in module sctools.test.test_fastq)
test_printing_string_record_generates_valid_fastq_record() (in module sctools.test.test_fastq)
test_reader_properly_subsets_based_on_indices() (in module sctools.test.test_fastq)
test_reader_reads_correct_number_of_records_across_multiple_files() (in module sctools.test.test_fastq)
test_reader_reads_first_record() (in module sctools.test.test_fastq)
test_reader_skips_header_character_raises_value_error() (in module sctools.test.test_fastq)
test_reader_stores_filenames() (in module sctools.test.test_fastq)
test_reads_barcodes_from_file() (in module sctools.test.test_barcode)
test_reads_mapped_exonic() (in module sctools.test.test_metrics)
test_reads_mapped_intronic() (in module sctools.test.test_metrics)
test_reads_mapped_uniquely() (in module sctools.test.test_metrics)
test_reads_mapped_utr() (in module sctools.test.test_metrics)
test_set_attribute_verify_included_in_output_string() (in module sctools.test.test_gtf)
test_single_read_evidence() (in module sctools.test.test_metrics)
test_sort_by_tags_and_queryname_sorts_correctly_from_file() (in module sctools.test.test_bam)
test_sort_by_tags_and_queryname_sorts_correctly_from_file_no_tag_keys() (in module sctools.test.test_bam)
test_sort_by_tags_and_queryname_sorts_correctly_no_tag_keys() (in module sctools.test.test_bam)
test_spliced_reads() (in module sctools.test.test_metrics)
test_split_bam() (in module sctools.test.test_entrypoints)
test_split_bam_raises_value_error_when_passed_bam_without_barcodes() (in module sctools.test.test_bam)
test_split_on_tagged_bam() (in module sctools.test.test_bam)
test_split_succeeds_with_raise_missing_false_and_no_cr_barcode_passed() (in module sctools.test.test_bam)
test_split_with_large_chunk_size_generates_one_file() (in module sctools.test.test_bam)
test_split_with_raise_missing_true_raises_warning_without_cr_barcode_passed() (in module sctools.test.test_bam)
test_str_and_int_chromosomes_both_function() (in module sctools.test.test_bam)
test_string_fastq_record_quality_score_parsing() (in module sctools.test.test_fastq)
test_summarize_hamming_distances_gives_reasonable_results() (in module sctools.test.test_barcode)
test_tag_sort_bam() (in module sctools.test.test_entrypoints)
test_tag_sort_bam_dash_t_specified_multiple_times() (in module sctools.test.test_entrypoints)
test_tag_sort_bam_no_tags() (in module sctools.test.test_entrypoints)
test_tag_sortable_record_eq_is_false_when_any_difference_exists() (in module sctools.test.test_bam)
test_tag_sortable_record_eq_is_true_for_identical_records() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_empty_query_name_is_smaller() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_empty_tag_is_smaller() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_is_false_for_equal_records() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_is_true_for_smaller_query_name() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_is_true_for_smaller_tag() (in module sctools.test.test_bam)
test_tag_sortable_record_lt_is_true_for_smaller_tag_regardless_of_query_name() (in module sctools.test.test_bam)
test_tag_sortable_record_missing_tag_value_is_empty_string() (in module sctools.test.test_bam)
test_tag_sortable_records_compare_correctly() (in module sctools.test.test_bam)
test_tag_sortable_records_raises_error_on_different_tag_lists() (in module sctools.test.test_bam)
test_tag_sortable_records_sort_correctly() (in module sctools.test.test_bam)
test_tag_sortable_records_sort_correctly_when_already_sorted() (in module sctools.test.test_bam)
test_tag_sortable_records_str() (in module sctools.test.test_bam)
test_three_bit_encode_decode_produces_same_string() (in module sctools.test.test_encodings)
test_three_bit_encoder_gets_correct_gc_content() (in module sctools.test.test_encodings)
test_three_bit_encodes_unknown_nucleotides_as_N() (in module sctools.test.test_encodings)
test_two_bit_encode_decode_produces_same_string_except_for_N() (in module sctools.test.test_encodings)
test_two_bit_encoder_gets_correct_gc_content() (in module sctools.test.test_encodings)
test_two_bit_throws_errors_when_asked_to_encode_unknown_nucleotide() (in module sctools.test.test_encodings)
test_verify_bam_sort() (in module sctools.test.test_entrypoints)
test_verify_bam_sort_raises_error_on_unsorted() (in module sctools.test.test_entrypoints)
test_verify_sort_on_unsorted_records_raises_error() (in module sctools.test.test_bam)
test_verify_sort_raises_no_error_on_sorted_records() (in module sctools.test.test_bam)
test_write_barcodes_to_bins() (in module sctools.test.test_bam)
test_zipping_readers_generates_expected_output() (in module sctools.test.test_fastq)
test_zipping_readers_with_indices_generates_expected_output() (in module sctools.test.test_fastq)
ThreeBit (class in sctools.encodings)
ThreeBit.ThreeBitEncodingMap (class in sctools.encodings)
trivial_whitelist() (in module sctools.test.test_barcode)
truncated_whitelist_from_10x() (in module sctools.test.test_barcode)
TwoBit (class in sctools.encodings)
TwoBit.TwoBitEncodingMap (class in sctools.encodings)
U
update() (sctools.stats.OnlineGaussianSufficientStatistic method)
,
[1]
V
verify_bam_sort() (sctools.platform.BarcodePlatform class method)
(sctools.platform.GenericPlatform class method)
(sctools.platform.TenXV2 class method)
verify_sort() (in module sctools.bam)
W
with_traceback() (sctools.bam.SortError method)
write() (sctools.metrics.writer.MetricCSVWriter method)
,
[1]
write_barcodes_to_bins() (in module sctools.bam)
write_header() (sctools.metrics.writer.MetricCSVWriter method)
,
[1]
Z
zip_readers() (in module sctools)
(in module sctools.reader)
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