Mercurial > repos > nml > mykrobe_parser

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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 97945a3ad655f1a0f99f577d0d423124460d900a
author nml
date Tue, 24 Oct 2023 21:28:06 +0000
parents 8e7e5a660942
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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105 "_cls": "Call.VariantCall"
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109 "Amikacin": {
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110 "predict": "S"
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112 "Capreomycin": {
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113 "predict": "S"
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116 "phylogenetics": {
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117 "phylo_group": {
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118 "Mycobacterium_tuberculosis_complex": {
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119 "percent_coverage": 98.467,
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120 "median_depth": 332.0
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123 "sub_complex": {
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124 "Unknown": {
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127 }
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128 },
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129 "species": {
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130 "Mycobacterium_africanum": {
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134 },
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135 "lineage": {
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136 "lineage": [
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137 "lineage5"
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138 ],
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139 "calls_summary": {
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140 "lineage5": {
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141 "good_nodes": 1,
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142 "tree_depth": 1,
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143 "genotypes": {
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144 "lineage5": 1
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146 }
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147 },
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148 "calls": {
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149 "lineage5": {
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150 "lineage5": {
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151 "C1799921A": {
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152 "variant": "ref-C1799921A?var_name=C1799921A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C1799921A",
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153 "genotype": [
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154 1,
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156 ],
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157 "genotype_likelihoods": [
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158 -40869.16316992115,
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161 ],
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162 "info": {
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163 "coverage": {
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164 "reference": {
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165 "percent_coverage": 0.0,
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167 "min_non_zero_depth": 0,
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168 "kmer_count": 0,
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170 },
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171 "alternate": {
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175 "kmer_count": 6635,
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177 }
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178 },
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179 "expected_depths": [
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182 "contamination_depths": [],
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183 "filter": [],
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184 "conf": 40551
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185 },
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186 "_cls": "Call.VariantCall"
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187 }
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189 }
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191 }
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192 },
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193 "kmer": 21,
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194 "probe_sets": [
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195 "tb-species-170421.fasta.gz",
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196 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
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197 "tb.lineage.20200930.probes.fa.gz"
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198 ],
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199 "files": [
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200 "ERR2704812_1.fastq",
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201 "ERR2704812_2.fastq"
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203 "version": {
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207 "genotype_model": "kmer_count"
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208 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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