def setUp(self):
self.clear_directory()
martian.test_initialize(outfile(""))
self.args = {
'bam': infile("chr10.bam"),
'variants': "null",
'input': infile("chr10.vcf")
}
def setUp(self):
self.clear_directory()
martian.test_initialize(outfile(""))
self.args = {
'reference_path': 'hg19',
'bam_file': infile("hg19_small.bam"),
'ground_truth': infile("gt_sort.vcf.gz"),
'input': infile("call_sort.vcf.gz"),
'genes_file': infile("small_refseq_genes.tsv"),
'long_switch_penalty_multiple': 5 }
def setUp(self):
#self.clear_directory()
martian.test_initialize(outfile(''))
self.args = {
'max_frac_black': 0.1,
'min_dist_from_black': 10000,
'seg_dup_min_dist': 10000,
'min_sv_len': 1,
'qv': 50,
'variants': infile('test_analyze_sv_calls2.bedpe'),
'gt_variants': infile('test_analyze_sv_calls_gt2.bedpe'),
'sv_blacklist_regions': infile('test_empty_blacklist.bed'),
'seg_dups': infile('test_empty_seg_dups.bedpe'),
}
def setUp(self):
martian.test_initialize(outfile(""))
self.in_files = pick_files("demultiplex/demultiplex/*.fastq.gz")
# Currently the demultiplexer always interleaves
base_args = {
'sample_index_error_rate': 0.15,
'interleave': 'true',
'rc_i2_read': 'false',
'si_read_type': 'I1'
}
self.args = base_args.copy()
self.args['raw_fastq_path'] = infile("demultiplex/demultiplex")
self.args_gz = base_args.copy()
self.args_gz['raw_fastq_path'] = infile("demultiplex/demultiplex_gz")
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
import os
import tenkit.test as tk_test
import tenkit.fasta as tk_fasta
import martian
from .. import *
martian.test_initialize(tk_test.out_path(""))
IN_PREFIX = tk_test.in_path('combine_and_trim_reads')
IN_RA_ALL = [
tk_test.in_path(
'combine_and_trim_reads/read-RA_si-AAAA_lane-1_chunk-1.fastq'),
tk_test.in_path(
'combine_and_trim_reads/read-RA_si-AAAN_lane-1_chunk-1.fastq'),
tk_test.in_path(
'combine_and_trim_reads/read-RA_si-CCCC_lane-1_chunk-1.fastq')
]
class TestFunctions(tk_test.UnitTestBase):
def test_setup_chunks(self):
args = martian.Record({
'input_mode':
'BCL_PROCESSOR',
'sample_def': [{
'read_path': IN_PREFIX,
'sample_indices': ["AAAA", "CCCC"],
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
import tenkit.test as tk_test
from .. import *
import crdna.bio_io as crdna_io
import pysam
import itertools
import numpy as np
import tenkit.constants
import crdna.read_filter
import martian
martian.test_initialize("")
# Patrick Marks
# Simple test of deduper
IN_BAM = tk_test.in_path('test_analyze_bias.bam')
OUT_BAM = tk_test.out_path('test_dedup_out.bam')
OUT_JSON = tk_test.out_path( 'test_dedup_summary.json')
IN_BAM_BIG = tk_test.in_path("test_mark_duplicates.bam")
class TestFunctions(tk_test.UnitTestBase):
def setUp(self):
pass
def test_dedup(self):
tenkit.constants.DUPLICATE_SUBSAMPLE_COVERAGES = [0.00001, 0.0001]
args = martian.Record({ 'input': IN_BAM, 'estimated_coverage': 100.0, 'perfect_read_count': 1000, 'chunk_start':None, 'chunk_end':None })