| Next changeset 1:b8e3d957c0f5 (2020-09-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" |
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added:
plink.xml test-data/1.tabular test-data/out.assoc.bed test-data/out.assoc.bim test-data/out.assoc.fam test-data/out.assoc.fisher test-data/out.assoc.fisher.adjusted test-data/out.assoc.fisher.mperm test-data/out.assoc.logistic test-data/out.assoc.logistic.adjusted test-data/out.assoc.logistic.perm test-data/out.freq test-data/out.genome test-data/out.hardy test-data/out.het test-data/out.imiss test-data/out.lmiss test-data/out.map test-data/out.ped test-data/out.sexcheck test-data/plink.bed test-data/plink.bim test-data/plink.cluster1 test-data/plink.cluster2 test-data/plink.cluster3 test-data/plink.fam test-data/plink.genome test-data/plink.log test-data/plink.mds test-data/plink.mds.eigenval test-data/plink.prune.in test-data/plink_2.bed test-data/plink_2.bim test-data/plink_2.fam test-data/plink_2.log test-data/plink_log.txt test-data/plink_output.log test-data/plink_test.bim test-data/plinke.genome test-data/stats.bed test-data/stats.bim test-data/stats.fam test-data/stats.log test-data/test.vcf test-data/test1_out.bed test-data/test1_out.bim test-data/test1_out.fam test-data/test2_out.bed test-data/test2_out.bim test-data/test2_out.fam test-data/test5_out.bed test-data/test5_out.bim test-data/test5_out.fam test-data/test6_out.bed test-data/test6_out.bim test-data/test6_out.fam test-data/testing.txt test-data/update_cols.txt test-data/vcf_out.bed test-data/vcf_out.bim test-data/vcf_out.fam test-data/x_plink.bim |
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| diff -r 000000000000 -r a98caf1d69ab plink.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plink.xml Mon Sep 21 10:09:22 2020 +0000 |
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| b"@@ -0,0 +1,1368 @@\n+<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>\n+ <macros>\n+ <token name='@TOOL_VERSION@'>1.9.b618</token>\n+ <token name='@VERSION_SUFFIX@'>0</token>\n+ <xml name='template_sanitizer'>\n+ <sanitizer>\n+ <valid initial='default'>\n+ <add value='#' />\n+ <add value='@' />\n+ <add value='$'/>\n+ <add value='['/>\n+ <add value=']'/>\n+ <add value='\\'/>\n+ <remove value='"'/>\n+ <remove value='''/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+ <xml name='chr_sanitizer'>\n+ <sanitizer>\n+ <valid initial='string.digits'>\n+ <add value='X' />\n+ <add value='Y' />\n+ <add value=' ' />\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+ <xml name='snp_sanitizer'>\n+ <sanitizer>\n+ <valid initial='string.ascii_letters + string.digits'/>\n+ </sanitizer>\n+ </xml>\n+ <xml name='snp_space_sanitizer'>\n+ <sanitizer>\n+ <valid initial='string.ascii_letters + string.digits'>\n+ <add value=' '/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type='package' version='1.90b6.18'>plink</requirement>\n+ </requirements>\n+ <command detect_errors='exit_code'><![CDATA[\n+\n+ ## Create Plink folder for any inputs\n+ mkdir ./plink_output\n+ && mkdir ./plink_input\n+ #if $inputs.inputs.filetype == 'bfile':\n+ && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed\n+ && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim\n+ && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam\n+ #elif $inputs.inputs.filetype == 'vcf':\n+ #if $inputs.inputs.input.is_of_type('vcf'):\n+ && plink --vcf '$inputs.inputs.input' \n+ #else:\n+ && plink --bcf '$inputs.inputs.input' \n+ #end if\n+ --out plink_input/plink_input\n+ #end if\n+\n+ ## If bmerge is set, create folder for merged files\n+ #if $functions.func == 'data_manage':\n+ #if $functions.bmerge.set == 'Yes':\n+ && mkdir bmerge_files\n+ && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed\n+ && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim\n+ && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam\n+ #end if\n+ #end if\n+\n+ ## Plink commands by section\n+\n+ && plink --bfile plink_input/plink_input\n+ #if $inputs.covar_input:\n+ --covar '$inputs.covar_input'\n+ #end if\n+ #if $inputs.pheno:\n+ --pheno $inputs.pheno\n+ #end if\n+ #if $functions.func == 'filtering':\n+ ##ID list functions\n+ #if $functions.id_list.func == 'keep':\n+ --keep '$functions.id_list.file'\n+ #elif $functions.id_list.func == 'keep-fam':\n+ --keep-fam '$functions.id_list.file'\n+ #elif $functions.id_list.func == 'remove':\n+ --remove '$functions.id_list.file'\n+ #elif $functions.id_list.func == 'remove-fam':\n+ --remove-fam '$functions.id_list.file'\n+ #end if\n+\n+ ##Extraction \n+ #if $functions.extraction.ex_func == 'extract':\n+ --extract $functions.extraction.range $functions.extraction.file\n+ #elif $functions.extraction.ex_func == 'exclude':\n+ --exclude $functions.extraction.range $functions.extraction.file\n+ #end if\n+\n+ ##Chromosome-specificity\n+ #if $functions.chromosome:\n+ --chr $functions.chromosome\n+ #end if\n+\n+ #if $functions.excluded_chromosome:\n+ --"..b'n name=\'inputs\'>\n+ <conditional name=\'inputs\'>\n+ <param name=\'filetype\' value=\'bfile\'/>\n+ <param name=\'bed\' value=\'plink.bed\'/>\n+ <param name=\'bim\' value=\'plink.bim\'/>\n+ <param name=\'fam\' value=\'plink.fam\'/>\n+ </conditional>\n+ </section>\n+ <conditional name=\'functions\'>\n+ <param name=\'func\' value=\'association\'/>\n+ <conditional name=\'assoc\'>\n+ <param name=\'assoc\' value=\'Yes\'/>\n+ <conditional name=\'perm\'>\n+ <param name=\'perm\' value=\'mperm\'/>\n+ <param name=\'value\' value=\'10000\'/>\n+ </conditional>\n+ <param name=\'fisher\' value=\'fisher-midp\'/>\n+ </conditional>\n+ <conditional name=\'adjust\'>\n+ <param name=\'adjust\' value=\'Yes\'/>\n+ <param name=\'tests\' value=\'gc,log10,qq-plot\'/>\n+ </conditional>\n+ <conditional name=\'logistic\'>\n+ <param name=\'logistic\' value=\'Yes\'/>\n+ <conditional name=\'perm\'>\n+ <param name=\'perm\' value=\'perm\'/>\n+ </conditional>\n+ <param name=\'genedrop\' value=\'genedrop\'/>\n+ <param name=\'perm_count\' value=\'perm-count\'/>\n+ <param name=\'dominance\' value=\'dominant\'/>\n+ <param name=\'hide_covar\' value=\'hide-covar\'/>\n+ <param name=\'beta\' value=\'beta\'/>\n+ <param name=\'intercept\' value=\'intercept\'/>\n+ </conditional>\n+ <param name=\'lambda\' value=\'1.0\'/>\n+ </conditional>\n+ <output_collection name=\'plink_out\' type=\'list\'>\n+ <element name=\'plink_bed\' file=\'out.assoc.bed\' compare=\'sim_size\'/>\n+ <element name=\'plink_bim\' file=\'out.assoc.bim\'/>\n+ <element name=\'plink_fam\' file=\'out.assoc.fam\'/>\n+ </output_collection>\n+ <output name=\'fisher\' value="out.assoc.fisher"/>\n+ <output name=\'adjust_fisher\' value="out.assoc.fisher.adjusted" sort="True" />\n+ <output name=\'fisher_mperm\' value="out.assoc.fisher.mperm" compare=\'sim_size\'/>\n+ <output name=\'logistic\' value="out.assoc.logistic"/>\n+ <output name=\'adjust_logistic\' value="out.assoc.logistic.adjusted"/>\n+ <output name=\'logistic_perm\' value="out.assoc.logistic.perm" compare=\'sim_size\'/>\n+ </test>\n+\n+ <test expect_num_outputs=\'6\'>\n+ <section name=\'inputs\'>\n+ <conditional name=\'inputs\'>\n+ <param name=\'filetype\' value=\'bfile\'/>\n+ <param name=\'bed\' value=\'plink.bed\'/>\n+ <param name=\'bim\' value=\'plink.bim\'/>\n+ <param name=\'fam\' value=\'plink.fam\'/>\n+ </conditional>\n+ </section>\n+ <conditional name=\'functions\'>\n+ <param name=\'func\' value=\'ibd\'/>\n+ <conditional name=\'genome\'>\n+ <param name=\'output_genome\' value=\'Yes\'/>\n+ <param name=\'min\' value=\'0.1\'/>\n+ <param name=\'max\' value=\'0.9\'/>\n+ <param name=\'modifiers\' value=\'full,unbounded,nudge\'/>\n+ </conditional>\n+ </conditional>\n+ <output name=\'genome\' file=\'out.genome\'/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.\n+\n+ For detailed usage notes, visit http://www.cog-genomics.org/plink/2.0/\n+ ]]></help>\n+ <citations>\n+ <citation type=\'doi\'>10.1186/s13742-015-0047-8</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r a98caf1d69ab test-data/1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.tabular Mon Sep 21 10:09:22 2020 +0000 |
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| @@ -0,0 +1,6 @@ +chr22 1000 NM_17 +chr22 2000 NM_18 +chr10 2200 NM_10 +chr10 hap test +chr10 1200 NM_11 +chr22 1600 NM_19 \ No newline at end of file |
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| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.bed |
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| Binary file test-data/out.assoc.bed has changed |
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| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.bim Mon Sep 21 10:09:22 2020 +0000 |
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| @@ -0,0 +1,50 @@ +1 snp0 0 0 A B +1 snp1 0 1 A B +1 snp2 0 2 A B +1 snp3 0 3 B A +1 snp4 0 4 B A +1 snp5 0 5 B A +1 snp6 0 6 A B +1 snp7 0 7 A B +1 snp8 0 8 B A +1 snp9 0 9 A B +1 snp10 0 10 B A +1 snp11 0 11 B A +1 snp12 0 12 B A +1 snp13 0 13 A B +1 snp14 0 14 B A +1 snp15 0 15 A B +1 snp16 0 16 A B +1 snp17 0 17 B A +1 snp18 0 18 B A +1 snp19 0 19 A B +1 snp20 0 20 A B +1 snp21 0 21 A B +1 snp22 0 22 A B +1 snp23 0 23 B A +1 snp24 0 24 A B +1 snp25 0 25 A B +1 snp26 0 26 B A +1 snp27 0 27 A B +1 snp28 0 28 B A +1 snp29 0 29 B A +1 snp30 0 30 A B +1 snp31 0 31 B A +1 snp32 0 32 B A +1 snp33 0 33 A B +1 snp34 0 34 B A +1 snp35 0 35 B A +1 snp36 0 36 A B +1 snp37 0 37 A B +1 snp38 0 38 B A +1 snp39 0 39 B A +1 snp40 0 40 B A +1 snp41 0 41 B A +1 snp42 0 42 B A +1 snp43 0 43 A B +1 snp44 0 44 A B +1 snp45 0 45 A B +1 snp46 0 46 A B +1 snp47 0 47 B A +1 snp48 0 48 B A +1 snp49 0 49 A B |
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| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.fam Mon Sep 21 10:09:22 2020 +0000 |
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| @@ -0,0 +1,200 @@ +per0 per0 0 0 2 1 +per1 per1 0 0 2 2 +per2 per2 0 0 2 1 +per3 per3 0 0 2 1 +per4 per4 0 0 2 1 +per5 per5 0 0 2 1 +per6 per6 0 0 2 2 +per7 per7 0 0 2 2 +per8 per8 0 0 2 1 +per9 per9 0 0 2 1 +per10 per10 0 0 2 1 +per11 per11 0 0 2 2 +per12 per12 0 0 2 1 +per13 per13 0 0 2 2 +per14 per14 0 0 2 2 +per15 per15 0 0 2 1 +per16 per16 0 0 2 2 +per17 per17 0 0 2 2 +per18 per18 0 0 2 1 +per19 per19 0 0 2 2 +per20 per20 0 0 2 2 +per21 per21 0 0 2 2 +per22 per22 0 0 2 2 +per23 per23 0 0 2 2 +per24 per24 0 0 2 1 +per25 per25 0 0 2 1 +per26 per26 0 0 2 2 +per27 per27 0 0 2 2 +per28 per28 0 0 2 2 +per29 per29 0 0 2 2 +per30 per30 0 0 2 2 +per31 per31 0 0 2 2 +per32 per32 0 0 2 2 +per33 per33 0 0 2 1 +per34 per34 0 0 2 1 +per35 per35 0 0 2 1 +per36 per36 0 0 2 2 +per37 per37 0 0 2 2 +per38 per38 0 0 2 2 +per39 per39 0 0 2 1 +per40 per40 0 0 2 1 +per41 per41 0 0 2 1 +per42 per42 0 0 2 2 +per43 per43 0 0 2 2 +per44 per44 0 0 2 2 +per45 per45 0 0 2 2 +per46 per46 0 0 2 2 +per47 per47 0 0 2 2 +per48 per48 0 0 2 1 +per49 per49 0 0 2 1 +per50 per50 0 0 2 2 +per51 per51 0 0 2 1 +per52 per52 0 0 2 2 +per53 per53 0 0 2 1 +per54 per54 0 0 2 2 +per55 per55 0 0 2 1 +per56 per56 0 0 2 2 +per57 per57 0 0 2 2 +per58 per58 0 0 2 2 +per59 per59 0 0 2 1 +per60 per60 0 0 2 2 +per61 per61 0 0 2 2 +per62 per62 0 0 2 2 +per63 per63 0 0 2 1 +per64 per64 0 0 2 1 +per65 per65 0 0 2 2 +per66 per66 0 0 2 2 +per67 per67 0 0 2 1 +per68 per68 0 0 2 2 +per69 per69 0 0 2 1 +per70 per70 0 0 2 2 +per71 per71 0 0 2 2 +per72 per72 0 0 2 2 +per73 per73 0 0 2 1 +per74 per74 0 0 2 2 +per75 per75 0 0 2 1 +per76 per76 0 0 2 2 +per77 per77 0 0 2 2 +per78 per78 0 0 2 1 +per79 per79 0 0 2 2 +per80 per80 0 0 2 1 +per81 per81 0 0 2 2 +per82 per82 0 0 2 1 +per83 per83 0 0 2 1 +per84 per84 0 0 2 1 +per85 per85 0 0 2 2 +per86 per86 0 0 2 1 +per87 per87 0 0 2 2 +per88 per88 0 0 2 1 +per89 per89 0 0 2 2 +per90 per90 0 0 2 2 +per91 per91 0 0 2 1 +per92 per92 0 0 2 2 +per93 per93 0 0 2 1 +per94 per94 0 0 2 2 +per95 per95 0 0 2 2 +per96 per96 0 0 2 2 +per97 per97 0 0 2 1 +per98 per98 0 0 2 2 +per99 per99 0 0 2 2 +per100 per100 0 0 2 2 +per101 per101 0 0 2 2 +per102 per102 0 0 2 1 +per103 per103 0 0 2 1 +per104 per104 0 0 2 1 +per105 per105 0 0 2 2 +per106 per106 0 0 2 2 +per107 per107 0 0 2 2 +per108 per108 0 0 2 2 +per109 per109 0 0 2 1 +per110 per110 0 0 2 1 +per111 per111 0 0 2 1 +per112 per112 0 0 2 2 +per113 per113 0 0 2 1 +per114 per114 0 0 2 2 +per115 per115 0 0 2 1 +per116 per116 0 0 2 1 +per117 per117 0 0 2 2 +per118 per118 0 0 2 2 +per119 per119 0 0 2 2 +per120 per120 0 0 2 2 +per121 per121 0 0 2 1 +per122 per122 0 0 2 2 +per123 per123 0 0 2 1 +per124 per124 0 0 2 1 +per125 per125 0 0 2 1 +per126 per126 0 0 2 2 +per127 per127 0 0 2 1 +per128 per128 0 0 2 2 +per129 per129 0 0 2 2 +per130 per130 0 0 2 2 +per131 per131 0 0 2 2 +per132 per132 0 0 2 2 +per133 per133 0 0 2 2 +per134 per134 0 0 2 1 +per135 per135 0 0 2 1 +per136 per136 0 0 2 1 +per137 per137 0 0 2 1 +per138 per138 0 0 2 1 +per139 per139 0 0 2 1 +per140 per140 0 0 2 1 +per141 per141 0 0 2 1 +per142 per142 0 0 2 1 +per143 per143 0 0 2 1 +per144 per144 0 0 2 2 +per145 per145 0 0 2 2 +per146 per146 0 0 2 1 +per147 per147 0 0 2 2 +per148 per148 0 0 2 2 +per149 per149 0 0 2 2 +per150 per150 0 0 2 1 +per151 per151 0 0 2 2 +per152 per152 0 0 2 1 +per153 per153 0 0 2 2 +per154 per154 0 0 2 2 +per155 per155 0 0 2 1 +per156 per156 0 0 2 1 +per157 per157 0 0 2 1 +per158 per158 0 0 2 2 +per159 per159 0 0 2 1 +per160 per160 0 0 2 2 +per161 per161 0 0 2 1 +per162 per162 0 0 2 2 +per163 per163 0 0 2 1 +per164 per164 0 0 2 2 +per165 per165 0 0 2 2 +per166 per166 0 0 2 1 +per167 per167 0 0 2 1 +per168 per168 0 0 2 1 +per169 per169 0 0 2 1 +per170 per170 0 0 2 2 +per171 per171 0 0 2 1 +per172 per172 0 0 2 1 +per173 per173 0 0 2 1 +per174 per174 0 0 2 1 +per175 per175 0 0 2 2 +per176 per176 0 0 2 2 +per177 per177 0 0 2 2 +per178 per178 0 0 2 1 +per179 per179 0 0 2 1 +per180 per180 0 0 2 1 +per181 per181 0 0 2 1 +per182 per182 0 0 2 1 +per183 per183 0 0 2 1 +per184 per184 0 0 2 1 +per185 per185 0 0 2 1 +per186 per186 0 0 2 2 +per187 per187 0 0 2 1 +per188 per188 0 0 2 1 +per189 per189 0 0 2 2 +per190 per190 0 0 2 1 +per191 per191 0 0 2 1 +per192 per192 0 0 2 1 +per193 per193 0 0 2 2 +per194 per194 0 0 2 2 +per195 per195 0 0 2 1 +per196 per196 0 0 2 1 +per197 per197 0 0 2 1 +per198 per198 0 0 2 1 +per199 per199 0 0 2 2 |
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| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.fisher --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.fisher Mon Sep 21 10:09:22 2020 +0000 |
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| @@ -0,0 +1,51 @@ + CHR SNP BP A1 F_A F_U A2 P OR + 1 snp0 0 A 0.4802 0.4596 B 0.6532 1.086 + 1 snp1 1 A 0.4406 0.5354 B 0.06498 0.6836 + 1 snp2 2 A 0.4604 0.5152 B 0.2952 0.803 + 1 snp3 3 B 0.495 0.4848 A 0.8032 1.042 + 1 snp4 4 B 0.4901 0.5051 A 0.8034 0.9419 + 1 snp5 5 B 0.5198 0.4394 A 0.09971 1.381 + 1 snp6 6 A 0.5 0.5 B 0.9602 1 + 1 snp7 7 A 0.505 0.4848 B 0.6538 1.084 + 1 snp8 8 B 0.505 0.4596 A 0.3434 1.199 + 1 snp9 9 A 0.4802 0.4394 B 0.3953 1.179 + 1 snp10 10 B 0.4752 0.4798 A 0.9603 0.9819 + 1 snp11 11 B 0.4604 0.4848 A 0.6534 0.9065 + 1 snp12 12 B 0.5 0.4444 A 0.2509 1.25 + 1 snp13 13 A 0.4406 0.5556 B 0.02482 0.6301 + 1 snp14 14 B 0.4752 0.5051 A 0.5837 0.8875 + 1 snp15 15 A 0.5099 0.4343 B 0.1217 1.355 + 1 snp16 16 A 0.4604 0.4798 B 0.7268 0.9251 + 1 snp17 17 B 0.4356 0.4899 A 0.2938 0.8038 + 1 snp18 18 B 0.5248 0.4596 A 0.1785 1.298 + 1 snp19 19 A 0.4604 0.5051 B 0.3967 0.8361 + 1 snp20 20 A 0.4802 0.5152 B 0.5173 0.8695 + 1 snp21 21 A 0.4554 0.5253 B 0.1783 0.7559 + 1 snp22 22 A 0.4356 0.5404 B 0.04083 0.6565 + 1 snp23 23 B 0.5198 0.4596 A 0.2128 1.273 + 1 snp24 24 A 0.4802 0.4747 B 0.881 1.022 + 1 snp25 25 A 0.4901 0.4747 B 0.727 1.063 + 1 snp26 26 B 0.4802 0.5051 A 0.6539 0.9053 + 1 snp27 27 A 0.495 0.4848 B 0.8032 1.042 + 1 snp28 28 B 0.4604 0.4141 A 0.3397 1.207 + 1 snp29 29 B 0.4505 0.4899 A 0.4539 0.8536 + 1 snp30 30 A 0.5099 0.4747 B 0.4548 1.151 + 1 snp31 31 B 0.4752 0.5202 A 0.3971 0.8353 + 1 snp32 32 B 0.4802 0.4646 A 0.7268 1.064 + 1 snp33 33 A 0.4356 0.5101 B 0.1476 0.7414 + 1 snp34 34 B 0.495 0.4646 A 0.5168 1.13 + 1 snp35 35 B 0.5198 0.4697 A 0.2954 1.222 + 1 snp36 36 A 0.4505 0.5253 B 0.1482 0.741 + 1 snp37 37 A 0.5 0.4697 B 0.5169 1.129 + 1 snp38 38 B 0.4455 0.4949 A 0.3428 0.82 + 1 snp39 39 B 0.4703 0.4899 A 0.7271 0.9245 + 1 snp40 40 B 0.505 0.4747 A 0.5171 1.129 + 1 snp41 41 B 0.4554 0.5152 A 0.2515 0.7872 + 1 snp42 42 B 0.4703 0.5101 A 0.4548 0.8527 + 1 snp43 43 A 0.5 0.4545 B 0.3432 1.2 + 1 snp44 44 A 0.505 0.4646 B 0.3967 1.175 + 1 snp45 45 A 0.4406 0.5505 B 0.032 0.6431 + 1 snp46 46 A 0.505 0.4899 B 0.7273 1.062 + 1 snp47 47 B 0.4604 0.4495 A 0.8024 1.045 + 1 snp48 48 B 0.4653 0.4949 A 0.5834 0.8881 + 1 snp49 49 A 0.4703 0.5101 B 0.4548 0.8527 |
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| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.fisher.adjusted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.fisher.adjusted Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP UNADJ GC QQ BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY + 1 snp13 1.369 1.369 2 0 0 0.05171 0.05171 0.05883 0 + 1 snp45 1.276 1.276 1.523 0 0 0.02964 0.03136 0.05883 0 + 1 snp22 1.188 1.188 1.301 0 0 0.01545 0.01771 0.05883 0 + 1 snp1 1.019 1.019 1.155 0 0 0.002837 0.003842 0.05883 0 + 1 snp5 0.8623 0.8623 1.046 0 0 0.0002697 0.000487 0.05883 0 + 1 snp15 0.7893 0.7893 0.9586 0 0 6.152e-05 0.0001493 0.05883 0 + 1 snp33 0.7185 0.7185 0.8861 0 0 1.07e-05 3.822e-05 0.05883 0 + 1 snp36 0.717 0.717 0.8239 0 0 1.028e-05 3.822e-05 0.05883 0 + 1 snp21 0.6489 0.6489 0.7696 0 0 1.314e-06 1.004e-05 0.05883 0 + 1 snp18 0.6487 0.6487 0.7212 0 0 1.303e-06 1.004e-05 0.05883 0 + 1 snp23 0.5838 0.5838 0.6778 0 0 1.195e-07 2.452e-06 0.05883 0 + 1 snp12 0.5228 0.5228 0.6383 0 0 7.772e-09 3.935e-07 0.05883 0 + 1 snp41 0.5219 0.5219 0.6021 0 0 7.455e-09 3.935e-07 0.05883 0 + 1 snp17 0.4642 0.4642 0.5686 0 0 3.191e-10 7.563e-08 0.05883 0 + 1 snp2 0.4625 0.4625 0.5376 0 0 2.869e-10 7.563e-08 0.05883 0 + 1 snp35 0.4622 0.4622 0.5086 0 0 2.825e-10 7.563e-08 0.05883 0 + 1 snp28 0.4103 0.4103 0.4815 0 0 8.864e-12 2.336e-08 0.05883 0 + 1 snp38 0.4069 0.4069 0.4559 0 0 6.895e-12 2.336e-08 0.05883 0 + 1 snp43 0.4064 0.4064 0.4318 0 0 6.662e-12 2.336e-08 0.05883 0 + 1 snp8 0.4062 0.4062 0.4089 0 0 6.539e-12 2.336e-08 0.05883 0 + 1 snp9 0.3537 0.3537 0.3872 0 0 8.607e-14 1.038e-08 0.05883 0 + 1 snp19 0.3524 0.3524 0.3665 0 0 7.618e-14 1.038e-08 0.05883 0 + 1 snp44 0.3523 0.3523 0.3468 0 0 7.575e-14 1.038e-08 0.05883 0 + 1 snp31 0.352 0.352 0.3279 0 0 7.348e-14 1.038e-08 0.05883 0 + 1 snp29 0.3018 0.3018 0.3098 0 0 4.339e-16 6.787e-09 0.05883 0 + 1 snp30 0.3011 0.3011 0.2924 0 0 3.857e-16 6.787e-09 0.05883 0 + 1 snp42 0.3011 0.3011 0.2757 0 0 3.857e-16 6.787e-09 0.05883 0 + 1 snp49 0.3011 0.3011 0.2596 0 0 3.857e-16 6.787e-09 0.05883 0 + 1 snp34 0.253 0.253 0.2441 0 0 0 6.732e-09 0.05883 0 + 1 snp37 0.2529 0.2529 0.2291 0 0 0 6.732e-09 0.05883 0 + 1 snp40 0.2528 0.2528 0.2147 0 0 0 6.732e-09 0.05883 0 + 1 snp20 0.2526 0.2526 0.2007 0 0 0 6.732e-09 0.05883 0 + 1 snp48 0.2072 0.2072 0.1871 0 0 0 6.732e-09 0.05814 0 + 1 snp14 0.207 0.207 0.1739 0 0 0 6.732e-09 0.05814 0 + 1 snp0 0.1643 0.1643 0.1612 0 0 0 4.076e-09 0.05814 0 + 1 snp11 0.1642 0.1642 0.1487 0 0 0 4.076e-09 0.05814 0 + 1 snp7 0.1639 0.1639 0.1367 0 0 0 4.076e-09 0.05814 0 + 1 snp26 0.1638 0.1638 0.1249 0 0 0 4.076e-09 0.05814 0 + 1 snp32 0.1235 0.1235 0.1135 0 0 0 4.076e-09 0.05814 0 + 1 snp16 0.1235 0.1235 0.1024 0 0 0 4.076e-09 0.05814 0 + 1 snp25 0.1234 0.1234 0.09151 0 0 0 4.076e-09 0.05814 0 + 1 snp39 0.1233 0.1233 0.08092 0 0 0 4.076e-09 0.05814 0 + 1 snp46 0.1233 0.1233 0.07058 0 0 0 4.076e-09 0.05814 0 + 1 snp47 0.08552 0.08552 0.06048 0 0 0 4.076e-09 0.05814 0 + 1 snp3 0.08512 0.08512 0.05061 0 0 0 4.076e-09 0.05814 0 + 1 snp27 0.08512 0.08512 0.04096 0 0 0 4.076e-09 0.05814 0 + 1 snp4 0.08501 0.08501 0.03152 0 0 0 4.076e-09 0.05814 0 + 1 snp24 0.04939 0.04939 0.02228 0 0 0 4.076e-09 0.03167 0 + 1 snp6 0.0159 0.0159 0.01323 0 0 0 4.076e-09 0.01585 0 + 1 snp10 0.01585 0.01585 0.004365 0 0 0 4.076e-09 0.01585 0 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.fisher.mperm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.fisher.mperm Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP EMP1 EMP2 + 1 snp0 0.6485 1 + 1 snp1 0.06724 0.9756 + 1 snp2 0.2894 1 + 1 snp3 0.8024 1 + 1 snp4 0.8102 1 + 1 snp5 0.08614 0.9971 + 1 snp6 0.9608 1 + 1 snp7 0.6315 1 + 1 snp8 0.3596 1 + 1 snp9 0.3878 1 + 1 snp10 0.9566 1 + 1 snp11 0.6523 1 + 1 snp12 0.2271 1 + 1 snp13 0.02575 0.7544 + 1 snp14 0.5918 1 + 1 snp15 0.1154 0.9996 + 1 snp16 0.7294 1 + 1 snp17 0.259 1 + 1 snp18 0.1944 1 + 1 snp19 0.3917 1 + 1 snp20 0.5198 1 + 1 snp21 0.1603 1 + 1 snp22 0.03675 0.8985 + 1 snp23 0.2278 1 + 1 snp24 0.8825 1 + 1 snp25 0.7269 1 + 1 snp26 0.6533 1 + 1 snp27 0.8142 1 + 1 snp28 0.3383 1 + 1 snp29 0.4681 1 + 1 snp30 0.458 1 + 1 snp31 0.3922 1 + 1 snp32 0.7283 1 + 1 snp33 0.1654 0.9999 + 1 snp34 0.5148 1 + 1 snp35 0.2918 1 + 1 snp36 0.165 0.9999 + 1 snp37 0.5271 1 + 1 snp38 0.3427 1 + 1 snp39 0.7368 1 + 1 snp40 0.5179 1 + 1 snp41 0.234 1 + 1 snp42 0.4554 1 + 1 snp43 0.3474 1 + 1 snp44 0.4033 1 + 1 snp45 0.02845 0.8325 + 1 snp46 0.7231 1 + 1 snp47 0.7953 1 + 1 snp48 0.5771 1 + 1 snp49 0.4793 1 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.logistic --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.logistic Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,101 @@\n+ CHR SNP BP A1 TEST NMISS BETA STAT P \n+ 1 snp0 0 A DOM 200 0.2307 0.7225 0.47\n+ 1 snp0 0 A INTERCEPT 200 -0.1484 NA NA\n+ 1 snp1 1 A DOM 200 -0.3807 -1.185 0.2359\n+ 1 snp1 1 A INTERCEPT 200 0.2985 NA NA\n+ 1 snp2 2 A DOM 200 -0.2859 -0.8822 0.3777\n+ 1 snp2 2 A INTERCEPT 200 0.2318 NA NA\n+ 1 snp3 3 B DOM 200 0.34 1.049 0.2942\n+ 1 snp3 3 B INTERCEPT 200 -0.2318 NA NA\n+ 1 snp4 4 B DOM 200 -0.278 -0.8685 0.3851\n+ 1 snp4 4 B INTERCEPT 200 0.2231 NA NA\n+ 1 snp5 5 B DOM 200 0.3479 1.059 0.2895\n+ 1 snp5 5 B INTERCEPT 200 -0.2412 NA NA\n+ 1 snp6 6 A DOM 200 -0.1934 -0.5824 0.5603\n+ 1 snp6 6 A INTERCEPT 200 0.1671 NA NA\n+ 1 snp7 7 A DOM 200 0.02564 0.07511 0.9401\n+ 1 snp7 7 A INTERCEPT 200 -4.356e-07 NA NA\n+ 1 snp8 8 B DOM 200 0.3263 1.031 0.3024\n+ 1 snp8 8 B INTERCEPT 200 -0.2151 NA NA\n+ 1 snp9 9 A DOM 200 -0.02257 -0.07127 0.9432\n+ 1 snp9 9 A INTERCEPT 200 0.03637 NA NA\n+ 1 snp10 10 B DOM 200 -0.08004 -0.2449 0.8065\n+ 1 snp10 10 B INTERCEPT 200 0.08004 NA NA\n+ 1 snp11 11 B DOM 200 -0.02257 -0.07126 0.9432\n+ 1 snp11 11 B INTERCEPT 200 0.03637 NA NA\n+ 1 snp12 12 B DOM 200 0.3972 1.215 0.2244\n+ 1 snp12 12 B INTERCEPT 200 -0.2763 NA NA\n+ 1 snp13 13 A DOM 200 -0.6692 -2.01 0.04445\n+ 1 snp13 13 A INTERCEPT 200 0.5213 NA NA\n+ 1 snp14 14 B DOM 200 -0.2301 -0.7156 0.4743\n+ 1 snp14 14 B INTERCEPT 200 0.1892 NA NA\n+ 1 snp15 15 A DOM 200 0.4455 1.369 0.1711\n+ 1 snp15 15 A INTERCEPT 200 -0.3102 NA NA\n+ 1 snp16 16 A DOM 200 -0.07146 -0.2268 0.8206\n+ 1 snp16 16 A INTERCEPT 200 0.07146 NA NA\n+ 1 snp17 17 B DOM 200 -0.5592 -1.692 0.0906\n+ 1 snp17 17 B INTERCEPT 200 0.4383 NA NA\n+ 1 snp18 18 B DOM 200 0.3263 1.031 0.3024\n+ 1 snp18 18 B INTERCEPT 200 -0.2151 NA NA\n+ 1 snp19 19 A DOM 200 -0.1312 -0.4039 0.6863\n+ 1 snp19 19 A INTERCEPT 200 0.1178 NA NA\n+ 1 snp20 20 A DOM 200 -0.4977 -1.522 0.1281\n+ 1 snp20 20 A INTERCEPT 200 0.3895 NA NA\n+ 1 snp21 21 A DOM 200 -0.4155 -1.241 0.2146\n+ 1 snp21 21 A INTERCEPT 200 0.3365 NA NA\n+ 1 snp22 22 A DOM 200 -0.5122 '..b' 1 snp27 27 A DOM 200 0.127 0.4031 0.6869\n+ 1 snp27 27 A INTERCEPT 200 -0.07146 NA NA\n+ 1 snp28 28 B DOM 200 0.2135 0.7029 0.4821\n+ 1 snp28 28 B INTERCEPT 200 -0.1252 NA NA\n+ 1 snp29 29 B DOM 200 -0.06669 -0.216 0.829\n+ 1 snp29 29 B INTERCEPT 200 0.06669 NA NA\n+ 1 snp30 30 A DOM 200 -0.1269 -0.3957 0.6924\n+ 1 snp30 30 A INTERCEPT 200 0.1133 NA NA\n+ 1 snp31 31 B DOM 200 -0.4507 -1.372 0.17\n+ 1 snp31 31 B INTERCEPT 200 0.3567 NA NA\n+ 1 snp32 32 B DOM 200 0.3263 1.031 0.3024\n+ 1 snp32 32 B INTERCEPT 200 -0.2151 NA NA\n+ 1 snp33 33 A DOM 200 -0.4069 -1.301 0.1934\n+ 1 snp33 33 A INTERCEPT 200 0.3075 NA NA\n+ 1 snp34 34 B DOM 200 0.1289 0.4045 0.6859\n+ 1 snp34 34 B INTERCEPT 200 -0.07411 NA NA\n+ 1 snp35 35 B DOM 200 0.246 0.7409 0.4587\n+ 1 snp35 35 B INTERCEPT 200 -0.1671 NA NA\n+ 1 snp36 36 A DOM 200 -0.4611 -1.463 0.1435\n+ 1 snp36 36 A INTERCEPT 200 0.3483 NA NA\n+ 1 snp37 37 A DOM 200 0.1782 0.5619 0.5742\n+ 1 snp37 37 A INTERCEPT 200 -0.1092 NA NA\n+ 1 snp38 38 B DOM 200 -0.3711 -1.169 0.2424\n+ 1 snp38 38 B INTERCEPT 200 0.2877 NA NA\n+ 1 snp39 39 B DOM 200 -0.2179 -0.6934 0.488\n+ 1 snp39 39 B INTERCEPT 200 0.1759 NA NA\n+ 1 snp40 40 B DOM 200 0.2907 0.8926 0.3721\n+ 1 snp40 40 B INTERCEPT 200 -0.1967 NA NA\n+ 1 snp41 41 B DOM 200 -0.1358 -0.4125 0.6799\n+ 1 snp41 41 B INTERCEPT 200 0.1226 NA NA\n+ 1 snp42 42 B DOM 200 -0.237 -0.7277 0.4668\n+ 1 snp42 42 B INTERCEPT 200 0.1967 NA NA\n+ 1 snp43 43 A DOM 200 0.2307 0.7225 0.47\n+ 1 snp43 43 A INTERCEPT 200 -0.1484 NA NA\n+ 1 snp44 44 A DOM 200 0.4929 1.521 0.1284\n+ 1 snp44 44 A INTERCEPT 200 -0.3429 NA NA\n+ 1 snp45 45 A DOM 200 -0.6426 -1.892 0.05845\n+ 1 snp45 45 A INTERCEPT 200 0.5108 NA NA\n+ 1 snp46 46 A DOM 200 0.1889 0.5734 0.5663\n+ 1 snp46 46 A INTERCEPT 200 -0.1226 NA NA\n+ 1 snp47 47 B DOM 200 0.02857 0.09259 0.9262\n+ 1 snp47 47 B INTERCEPT 200 -4.27e-07 NA NA\n+ 1 snp48 48 B DOM 200 -0.4383 -1.353 0.1762\n+ 1 snp48 48 B INTERCEPT 200 0.3429 NA NA\n+ 1 snp49 49 A DOM 200 -0.06899 -0.2213 0.8249\n+ 1 snp49 49 A INTERCEPT 200 0.06899 NA NA\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.logistic.adjusted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.logistic.adjusted Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP UNADJ GC QQ BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY + 1 snp13 1.206 1.206 2 0 0 0.01789 0.01789 0.07645 0 + 1 snp45 1.102 1.102 1.523 0 0 0.00711 0.007727 0.07645 0 + 1 snp17 0.9342 0.9342 1.301 0 0 0.0008958 0.001148 0.07645 0 + 1 snp22 0.8183 0.8183 1.155 0 0 0.0001145 0.0001877 0.07645 0 + 1 snp20 0.8014 0.8014 1.046 0 0 8.017e-05 0.0001595 0.07645 0 + 1 snp44 0.8006 0.8006 0.9586 0 0 7.882e-05 0.0001595 0.07645 0 + 1 snp36 0.7579 0.7579 0.8861 0 0 2.957e-05 9.353e-05 0.07645 0 + 1 snp31 0.6928 0.6928 0.8239 0 0 5.183e-06 2.534e-05 0.07645 0 + 1 snp15 0.6903 0.6903 0.7696 0 0 4.808e-06 2.534e-05 0.07645 0 + 1 snp48 0.6789 0.6789 0.7212 0 0 3.424e-06 2.534e-05 0.07645 0 + 1 snp33 0.6431 0.6431 0.6778 0 0 1.081e-06 1.427e-05 0.07645 0 + 1 snp21 0.603 0.603 0.6383 0 0 2.545e-07 5.98e-06 0.07645 0 + 1 snp12 0.5857 0.5857 0.6021 0 0 1.294e-07 4.766e-06 0.07645 0 + 1 snp1 0.5664 0.5664 0.5686 0 0 5.787e-08 3.548e-06 0.07645 0 + 1 snp38 0.556 0.556 0.5376 0 0 3.669e-08 3.508e-06 0.07645 0 + 1 snp5 0.4872 0.4872 0.5086 0 0 1.204e-09 4.444e-07 0.07645 0 + 1 snp3 0.481 0.481 0.4815 0 0 8.504e-10 4.444e-07 0.07645 0 + 1 snp8 0.4704 0.4704 0.4559 0 0 4.595e-10 4.444e-07 0.07645 0 + 1 snp32 0.4704 0.4704 0.4318 0 0 4.595e-10 4.444e-07 0.07645 0 + 1 snp18 0.4704 0.4704 0.4089 0 0 4.595e-10 4.444e-07 0.07645 0 + 1 snp40 0.3898 0.3898 0.3872 0 0 1.868e-12 6.575e-08 0.07645 0 + 1 snp2 0.384 0.384 0.3665 0 0 1.173e-12 6.575e-08 0.07645 0 + 1 snp4 0.3765 0.3765 0.3468 0 0 6.289e-13 6.575e-08 0.07645 0 + 1 snp35 0.3083 0.3083 0.3279 0 0 8.679e-16 5.034e-09 0.07645 0 + 1 snp26 0.3015 0.3015 0.3098 0 0 3.857e-16 5.034e-09 0.07645 0 + 1 snp42 0.3015 0.3015 0.2924 0 0 3.857e-16 5.034e-09 0.07645 0 + 1 snp43 0.2988 0.2988 0.2757 0 0 2.893e-16 5.034e-09 0.07645 0 + 1 snp0 0.2988 0.2988 0.2596 0 0 2.893e-16 5.034e-09 0.07645 0 + 1 snp14 0.2953 0.2953 0.2441 0 0 1.929e-16 5.034e-09 0.07645 0 + 1 snp28 0.2888 0.2888 0.2291 0 0 9.643e-17 5.034e-09 0.07645 0 + 1 snp39 0.2841 0.2841 0.2147 0 0 4.822e-17 5.034e-09 0.07645 0 + 1 snp6 0.23 0.23 0.2007 0 0 0 5.034e-09 0.06545 0 + 1 snp46 0.2257 0.2257 0.1871 0 0 0 5.034e-09 0.06545 0 + 1 snp25 0.2219 0.2219 0.1739 0 0 0 5.034e-09 0.06545 0 + 1 snp37 0.2203 0.2203 0.1612 0 0 0 5.034e-09 0.06545 0 + 1 snp41 0.1538 0.1538 0.1487 0 0 0 5.034e-09 0.04969 0 + 1 snp34 0.1503 0.1503 0.1367 0 0 0 5.034e-09 0.04969 0 + 1 snp19 0.1501 0.1501 0.1249 0 0 0 5.034e-09 0.04969 0 + 1 snp27 0.1497 0.1497 0.1135 0 0 0 5.034e-09 0.04969 0 + 1 snp30 0.1466 0.1466 0.1024 0 0 0 5.034e-09 0.04969 0 + 1 snp10 0.08608 0.08608 0.09151 0 0 0 5.034e-09 0.03893 0 + 1 snp24 0.08365 0.08365 0.08092 0 0 0 5.034e-09 0.03893 0 + 1 snp23 0.08136 0.08136 0.07058 0 0 0 5.034e-09 0.03893 0 + 1 snp16 0.07918 0.07918 0.06048 0 0 0 5.034e-09 0.03893 0 + 1 snp49 0.07711 0.07711 0.05061 0 0 0 5.034e-09 0.03893 0 + 1 snp29 0.07514 0.07514 0.04096 0 0 0 5.034e-09 0.03893 0 + 1 snp47 0.0308 0.0308 0.03152 0 0 0 5.034e-09 0.02352 0 + 1 snp7 0.02483 0.02483 0.02228 0 0 0 5.034e-09 0.02352 0 + 1 snp9 0.02352 0.02352 0.01323 0 0 0 5.034e-09 0.02352 0 + 1 snp11 0.02352 0.02352 0.004365 0 0 0 5.034e-09 0.02352 0 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.assoc.logistic.perm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.assoc.logistic.perm Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP EMP1 NP + 1 snp0 8 13 + 1 snp1 16.5 63 + 1 snp2 10 19 + 1 snp3 10 19 + 1 snp4 12 27 + 1 snp5 17 71 + 1 snp6 8 13 + 1 snp7 6 8 + 1 snp8 14 41 + 1 snp9 6 6 + 1 snp10 6 6 + 1 snp11 5 6 + 1 snp12 17.5 85 + 1 snp13 21.5 579 + 1 snp14 7 10 + 1 snp15 17.5 78 + 1 snp16 6 8 + 1 snp17 20.5 300 + 1 snp18 15 51 + 1 snp19 6 6 + 1 snp20 18.5 117 + 1 snp21 17 74 + 1 snp22 19.5 158 + 1 snp23 6 6 + 1 snp24 5 6 + 1 snp25 9 15 + 1 snp26 16 54 + 1 snp27 5 6 + 1 snp28 10 19 + 1 snp29 6 6 + 1 snp30 5 6 + 1 snp31 17 81 + 1 snp32 8 13 + 1 snp33 17.5 78 + 1 snp34 5 6 + 1 snp35 13 30 + 1 snp36 18 101 + 1 snp37 5 6 + 1 snp38 13 34 + 1 snp39 13 32 + 1 snp40 7 10 + 1 snp41 6 8 + 1 snp42 13 30 + 1 snp43 10 19 + 1 snp44 19 130 + 1 snp45 20.5 320 + 1 snp46 6 6 + 1 snp47 5 6 + 1 snp48 17 70 + 1 snp49 6 6 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.freq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.freq Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP A1 A2 MAF NCHROBS + 1 snp0 A B 0.47 400 + 1 snp1 A B 0.4875 400 + 1 snp2 A B 0.4875 400 + 1 snp3 B A 0.49 400 + 1 snp4 B A 0.4975 400 + 1 snp5 B A 0.48 400 + 1 snp6 A B 0.5 400 + 1 snp7 A B 0.495 400 + 1 snp8 B A 0.4825 400 + 1 snp9 A B 0.46 400 + 1 snp10 B A 0.4775 400 + 1 snp11 B A 0.4725 400 + 1 snp12 B A 0.4725 400 + 1 snp13 A B 0.4975 400 + 1 snp14 B A 0.49 400 + 1 snp15 A B 0.4725 400 + 1 snp16 A B 0.47 400 + 1 snp39 B A 0.4625 400 + 1 snp40 B A 0.4925 400 + 1 snp41 B A 0.4825 400 + 1 snp42 B A 0.4975 400 + 1 snp44 A B 0.49 400 + 1 snp46 A B 0.4875 400 + 1 snp48 B A 0.49 400 + 23 snp17 B A 0.4775 400 + 23 snp18 B A 0.4825 400 + 23 snp19 A B 0.4925 400 + 23 snp20 A B 0.49 400 + 23 snp21 A B 0.4375 400 + 23 snp22 A B 0.47 400 + 23 snp23 B A 0.4925 400 + 23 snp24 A B 0.4975 400 + 23 snp25 A B 0.4725 400 + 23 snp26 B A 0.4725 400 + 23 snp27 A B 0.48 400 + 23 snp28 B A 0.495 400 + 23 snp29 B A 0.4875 400 + 23 snp30 A B 0.485 400 + 23 snp31 B A 0.47 400 + 23 snp32 B A 0.48 400 + 23 snp33 A B 0.49 400 + 23 snp34 B A 0.485 400 + 23 snp35 B A 0.49 400 + 23 snp36 A B 0.4775 400 + 23 snp37 A B 0.485 400 + 23 snp38 B A 0.495 400 + 23 snp43 A B 0.4975 400 + 23 snp45 A B 0.455 400 + 23 snp47 B A 0.48 400 + 23 snp49 A B 0.49 400 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.genome --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.genome Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,6436 @@\n+ FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST PPC RATIO IBS0 IBS1 IBS2 HOMHOM HETHET\n+ per0 per0 per2 per2 UN NA 0.6391 0.5205 -0.1596 0.1006 -1 0.630000 0.0786 0.0000 4 29 17 1.0000 0.0000\n+ per0 per0 per10 per10 UN NA 0.7989 0.2010 0.0001 0.1006 -1 0.650000 0.0786 0.0000 5 25 20 1.0000 0.0000\n+ per0 per0 per16 per16 UN NA 0.4793 0.6002 -0.0796 0.2205 0 0.670000 0.7603 NA 3 27 20 0.0000 1.0000\n+ per0 per0 per18 per18 UN NA 0.6391 0.4805 -0.1197 0.1206 -1 0.640000 0.7603 NA 4 28 18 0.0000 1.0000\n+ per0 per0 per22 per22 UN NA 0.6391 0.3606 0.0002 0.1806 0 0.670000 0.7603 NA 4 25 21 0.0000 1.0000\n+ per0 per0 per24 per24 UN NA 0.4793 0.5603 -0.0396 0.2405 -1 0.680000 0.0786 0.0000 3 26 21 1.0000 0.0000\n+ per0 per0 per29 per29 UN NA 0.4793 0.6002 -0.0796 0.2205 0 0.670000 0.7603 NA 3 27 20 0.0000 1.0000\n+ per0 per0 per32 per32 UN NA 0.6715 0.2959 0.0326 0.1806 0 0.690000 0.0786 0.0000 5 21 24 1.0000 0.0000\n+ per0 per0 per40 per40 UN NA 0.4793 0.6002 -0.0796 0.2205 -1 0.670000 0.0786 0.0000 3 27 20 1.0000 0.0000\n+ per0 per0 per50 per50 UN NA 0.8089 0.1810 0.0101 0.1006 0 0.670000 0.0786 0.0000 6 21 23 1.0000 0.0000\n+ per0 per0 per51 per51 UN NA 0.4793 0.4803 0.0403 0.2805 -1 0.700000 0.7603 NA 3 24 23 0.0000 1.0000\n+ per0 per0 per56 per56 UN NA 0.7386 0.2416 0.0198 0.1406 0 0.690000 0.7603 NA 6 19 25 0.0000 1.0000\n+ per0 per0 per59 per59 UN NA 0.6391 0.3606 0.0002 0.1806 -1 0.670000 0.7603 NA 4 25 21 0.0000 1.0000\n+ per0 per0 per73 per73 UN NA 0.5768 0.3653 0.0578 0.2405 -1 0.720000 0.7603 NA 5 18 27 0.0000 1.0000\n+ per0 per0 per82 per82 UN NA 0.4793 0.6002 -0.0796 0.2205 -1 0.670000 0.7603 NA 3 27 20 0.0000 1.0000\n+ per0 per0 per84 per84 UN NA 0.6391 0.3207 0.0402 0.2005 -1 0.680000 0.7603 NA 4 24 22 0.0000 1.0000\n+ per0 per0 per88 per88 UN NA 0.4793 0.4404 0.0803 0.3005 -1 0.710000 0.7603 NA 3 23 24 0.0000 1.0000\n+ per0 per0 per94 per94 UN NA 0.6391 0.3207 0.0402 0.2005 0 0.700000 0.7603 NA 5 20 25 0.0000 1.0000\n+ per0 per0 per114 per114 UN NA 0.6076 0.3438 0.0486 0.2205 0 0.690000 0.7603 NA 4 23 23 0.0000 1.0000\n+ per0 per0 per119 per119 UN NA 0.6391 0.3207 0.0402 0.2005 0 0.700000 0.0786 0.0000 5 20 25 1.0000 0.0000\n+ per0 per0 per133 per133 UN NA 0.6391 0.3207 0.0402 0.2005 0 0.720000 0.0786 0.0000 6 16 28 1.0000 0.0000\n+ per0 per0 per136 per136 UN NA 0.4793 0.4803 0.0403 0.2805 -1 0.700000 0.7603 NA 3 24 23 0.0000 1.0000\n+ per0 per0 per141 per141 UN NA 0.6391 0.4805 -0.1197 0.1206 -1 0.640000 0.7603 NA 4 28 18 0.0000 1.0000\n+ per0 per0 per143 per143 UN NA 0.6391 0.5205 -0.1596 0.1006 -1 0.630000 0.7603 NA 4 29 17 0.0000 1.0000\n+ per0 per0 per162 per162 UN NA 0.6076 0.3438 0.0486 0.2205 0 0.690000 0.0786 0.0000 4 23 23 1.0000 0.0000\n+ per0 per0 per164 per164 UN NA 0.4793 0.7601 -0.2395 0.1406 0 0.630000 0.7603 NA 3 31 16 0.0000 1.0000\n+ per0 per0 per179 per179 UN NA 0.8089 0.1810 0.0101 0.1006 -1 0.670000 0.7603 NA 6 21 23 0.0000 1.0000\n+ per0 per0 per181 per181 UN'..b'86 0.0000 4 29 17 1.0000 0.0000\n+ per187 per187 per196 per196 UN NA 0.7733 0.2121 0.0145 0.1206 -1 0.660000 0.7603 NA 5 24 21 0.0000 1.0000\n+ per187 per187 per198 per198 UN NA 0.6391 0.4805 -0.1197 0.1206 -1 0.640000 0.0786 0.0000 4 28 18 1.0000 0.0000\n+ per188 per188 per192 per192 UN NA 0.7386 0.2416 0.0198 0.1406 -1 0.690000 0.0786 0.0000 6 19 25 1.0000 0.0000\n+ per188 per188 per194 per194 UN NA 0.4793 0.7202 -0.1995 0.1606 0 0.640000 0.7603 NA 3 30 17 0.0000 1.0000\n+ per188 per188 per196 per196 UN NA 0.4793 0.5603 -0.0396 0.2405 -1 0.680000 0.7603 NA 3 26 21 0.0000 1.0000\n+ per188 per188 per198 per198 UN NA 0.6391 0.3207 0.0402 0.2005 -1 0.700000 0.0786 0.0000 5 20 25 1.0000 0.0000\n+ per189 per189 per192 per192 UN NA 0.7386 0.2416 0.0198 0.1406 0 0.670000 0.7603 NA 5 23 22 0.0000 1.0000\n+ per189 per189 per193 per193 UN NA 0.4618 0.4355 0.1027 0.3205 1 0.720000 0.7603 NA 3 22 25 0.0000 1.0000\n+ per189 per189 per198 per198 UN NA 0.6391 0.4805 -0.1197 0.1206 0 0.640000 0.7603 NA 4 28 18 0.0000 1.0000\n+ per190 per190 per192 per192 UN NA 0.6391 0.3207 0.0402 0.2005 -1 0.700000 0.7603 NA 5 20 25 0.0000 1.0000\n+ per190 per190 per193 per193 UN NA 0.4793 0.5203 0.0004 0.2605 0 0.690000 0.7603 NA 3 25 22 0.0000 1.0000\n+ per190 per190 per194 per194 UN NA 0.6391 0.5205 -0.1596 0.1006 0 0.630000 0.7603 NA 4 29 17 0.0000 1.0000\n+ per190 per190 per196 per196 UN NA 0.8089 0.1810 0.0101 0.1006 -1 0.670000 0.7603 NA 6 21 23 0.0000 1.0000\n+ per190 per190 per198 per198 UN NA 0.4793 0.6002 -0.0796 0.2205 -1 0.670000 0.7603 NA 3 27 20 0.0000 1.0000\n+ per190 per190 per199 per199 UN NA 0.8089 0.1810 0.0101 0.1006 0 0.670000 0.7603 NA 6 21 23 0.0000 1.0000\n+ per191 per191 per194 per194 UN NA 0.4793 0.6402 -0.1196 0.2005 0 0.660000 0.0786 0.0000 3 28 19 1.0000 0.0000\n+ per191 per191 per198 per198 UN NA 0.4793 0.6402 -0.1196 0.2005 -1 0.660000 0.0786 0.0000 3 28 19 1.0000 0.0000\n+ per192 per192 per193 per193 UN NA 0.7386 0.2416 0.0198 0.1406 0 0.670000 0.7603 NA 5 23 22 0.0000 1.0000\n+ per192 per192 per196 per196 UN NA 0.6076 0.3438 0.0486 0.2205 -1 0.690000 0.7603 NA 4 23 23 0.0000 1.0000\n+ per192 per192 per197 per197 UN NA 0.3196 0.6400 0.0404 0.3604 -1 0.720000 0.7603 NA 2 24 24 0.0000 1.0000\n+ per192 per192 per199 per199 UN NA 0.3196 0.7599 -0.0795 0.3005 0 0.690000 0.7603 NA 2 27 21 0.0000 1.0000\n+ per193 per193 per196 per196 UN NA 0.4793 0.7202 -0.1995 0.1606 0 0.640000 0.7603 NA 3 30 17 0.0000 1.0000\n+ per193 per193 per197 per197 UN NA 0.6391 0.5205 -0.1596 0.1006 0 0.630000 0.7603 NA 4 29 17 0.0000 1.0000\n+ per193 per193 per198 per198 UN NA 0.4793 0.5603 -0.0396 0.2405 0 0.680000 0.7603 NA 3 26 21 0.0000 1.0000\n+ per195 per195 per196 per196 UN NA 0.6391 0.4406 -0.0797 0.1406 -1 0.650000 0.7603 NA 4 27 19 0.0000 1.0000\n+ per196 per196 per197 per197 UN NA 0.1598 1.0795 -0.2393 0.3005 -1 0.670000 0.7603 NA 1 31 18 0.0000 1.0000\n+ per196 per196 per198 per198 UN NA 0.6391 0.4805 -0.1197 0.1206 -1 0.640000 0.7603 NA 4 28 18 0.0000 1.0000\n+ per197 per197 per199 per199 UN NA 0.7386 0.2416 0.0198 0.1406 0 0.670000 0.7603 NA 5 23 22 0.0000 1.0000\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.hardy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.hardy Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,151 @@\n+ CHR SNP TEST A1 A2 GENO O(HET) E(HET) P \n+ 1 snp0 ALL A B 42/104/54 0.52 0.4982 0.5729\n+ 1 snp0 AFF A B 21/55/25 0.5446 0.4992 0.4284\n+ 1 snp0 UNAFF A B 21/49/29 0.4949 0.4967 1\n+ 1 snp1 ALL A B 49/97/54 0.485 0.4997 0.6729\n+ 1 snp1 AFF A B 19/51/31 0.505 0.4929 1\n+ 1 snp1 UNAFF A B 30/46/23 0.4646 0.4975 0.5457\n+ 1 snp2 ALL A B 47/101/52 0.505 0.4997 1\n+ 1 snp2 AFF A B 21/51/29 0.505 0.4969 1\n+ 1 snp2 UNAFF A B 26/50/23 0.5051 0.4995 1\n+ 1 snp3 ALL B A 48/100/52 0.5 0.4998 1\n+ 1 snp3 AFF B A 22/56/23 0.5545 0.5 0.3238\n+ 1 snp3 UNAFF B A 26/44/29 0.4444 0.4995 0.3141\n+ 1 snp4 ALL B A 53/93/54 0.465 0.5 0.3243\n+ 1 snp4 AFF B A 28/43/30 0.4257 0.4998 0.1627\n+ 1 snp4 UNAFF B A 25/50/24 0.5051 0.4999 1\n+ 1 snp5 ALL B A 42/108/50 0.54 0.4992 0.3209\n+ 1 snp5 AFF B A 26/53/22 0.5248 0.4992 0.6923\n+ 1 snp5 UNAFF B A 16/55/28 0.5556 0.4927 0.3064\n+ 1 snp6 ALL A B 48/104/48 0.52 0.5 0.6713\n+ 1 snp6 AFF A B 26/49/26 0.4851 0.5 0.8422\n+ 1 snp6 UNAFF A B 22/55/22 0.5556 0.5 0.3192\n+ 1 snp7 ALL A B 42/114/44 0.57 0.5 0.06552\n+ 1 snp7 AFF A B 23/56/22 0.5545 0.5 0.3238\n+ 1 snp7 UNAFF A B 19/58/22 0.5859 0.4995 0.1097\n+ 1 snp8 ALL B A 49/95/56 0.475 0.4994 0.4818\n+ 1 snp8 AFF B A 26/50/25 0.495 0.5 1\n+ 1 snp8 UNAFF B A 23/45/31 0.4545 0.4967 0.4204\n+ 1 snp9 ALL A B 39/106/55 0.53 0.4968 0.3944\n+ 1 snp9 AFF A B 24/49/28 0.4851 0.4992 0.8421\n+ 1 snp9 UNAFF A B 15/57/27 0.5758 0.4927 0.1518\n+ 1 snp10 ALL B A 41/109/50 0.545 0.499 0.2563\n+ 1 snp10 AFF B A 21/54/26 0.5347 0.4988 0.5519\n+ 1 snp10 UNAFF B A 20/55/24 0.5556 0.4992 0.3173\n+ 1 snp11 ALL B A 44/101/55 0.505 0.4985 0.8881\n+ 1 snp11 AFF B A 20/53/28 0.5248 0.4969 0.6894\n+ 1 snp11 UNAFF B A 24/48/27 0.4848 0.4995 0.8406\n+ 1 snp12 ALL B A 40/109/51 0.545 0.4985 0.2051\n+ 1 snp12 AFF B A 22/57/22 0.5644 0.5 0.2364\n+ 1 snp12 UNAFF B A 18/52/29 0.5253 0.4938 0.6836\n+ 1 snp13 ALL A B 50/99/51 0.495 0.5 0.8881\n+ 1 snp13 AFF A B 20/49/32 0.4851 0.4929 0.8426\n+ 1 snp13 UNAFF A B 30/50/19 0.5051 0.4938 1\n+ 1 snp14 ALL B A 49/98/53 0.49 0.4998 0.7784\n+ 1 snp14 AFF B A 24/48/29 0.4752 0.4988 0.6902\n+ 1 snp14 UNAFF B A 25/50/24 0.5051 0.4999 1\n+ 1 snp15 ALL A B 41/107/52 0.535 0.498'..b' 1\n+ 23 snp27 AFF A B 25/50/26 0.495 0.5 1\n+ 23 snp27 UNAFF A B 21/50/28 0.5051 0.4975 1\n+ 23 snp28 ALL B A 46/106/48 0.53 0.5 0.4793\n+ 23 snp28 AFF B A 26/53/22 0.5248 0.4992 0.6923\n+ 23 snp28 UNAFF B A 20/53/26 0.5354 0.4982 0.5469\n+ 23 snp29 ALL B A 53/89/58 0.445 0.4997 0.1213\n+ 23 snp29 AFF B A 24/43/34 0.4257 0.4951 0.1627\n+ 23 snp29 UNAFF B A 29/46/24 0.4646 0.4987 0.5458\n+ 23 snp30 ALL A B 49/96/55 0.48 0.4996 0.5736\n+ 23 snp30 AFF A B 26/49/26 0.4851 0.5 0.8422\n+ 23 snp30 UNAFF A B 23/47/29 0.4747 0.4982 0.6872\n+ 23 snp31 ALL B A 44/100/56 0.5 0.4982 1\n+ 23 snp31 AFF B A 21/48/32 0.4752 0.4941 0.6908\n+ 23 snp31 UNAFF B A 23/52/24 0.5253 0.4999 0.6904\n+ 23 snp32 ALL B A 49/94/57 0.47 0.4992 0.3988\n+ 23 snp32 AFF B A 25/45/31 0.4455 0.4982 0.3186\n+ 23 snp32 UNAFF B A 24/49/26 0.4949 0.4998 1\n+ 23 snp33 ALL A B 47/102/51 0.51 0.4998 0.8874\n+ 23 snp33 AFF A B 24/54/23 0.5347 0.5 0.5541\n+ 23 snp33 UNAFF A B 23/48/28 0.4848 0.4987 0.8405\n+ 23 snp34 ALL B A 43/108/49 0.54 0.4996 0.3213\n+ 23 snp34 AFF B A 17/58/26 0.5743 0.496 0.1599\n+ 23 snp34 UNAFF B A 26/50/23 0.5051 0.4995 1\n+ 23 snp35 ALL B A 47/102/51 0.51 0.4998 0.8874\n+ 23 snp35 AFF B A 22/51/28 0.505 0.4982 1\n+ 23 snp35 UNAFF B A 25/51/23 0.5152 0.4998 0.8421\n+ 23 snp36 ALL A B 45/101/54 0.505 0.499 1\n+ 23 snp36 AFF A B 25/51/25 0.505 0.5 1\n+ 23 snp36 UNAFF A B 20/50/29 0.5051 0.4959 1\n+ 23 snp37 ALL A B 47/100/53 0.5 0.4996 1\n+ 23 snp37 AFF A B 23/56/22 0.5545 0.5 0.3238\n+ 23 snp37 UNAFF A B 24/44/31 0.4444 0.4975 0.3136\n+ 23 snp38 ALL B A 46/106/48 0.53 0.5 0.4793\n+ 23 snp38 AFF B A 18/53/30 0.5248 0.4929 0.6859\n+ 23 snp38 UNAFF B A 28/53/18 0.5354 0.4949 0.5421\n+ 23 snp43 ALL A B 48/103/49 0.515 0.5 0.7772\n+ 23 snp43 AFF A B 24/54/23 0.5347 0.5 0.5541\n+ 23 snp43 UNAFF A B 24/49/26 0.4949 0.4998 1\n+ 23 snp45 ALL A B 42/98/60 0.49 0.496 0.8869\n+ 23 snp45 AFF A B 22/49/30 0.4851 0.4969 0.842\n+ 23 snp45 UNAFF A B 20/49/30 0.4949 0.4949 1\n+ 23 snp47 ALL B A 45/102/53 0.51 0.4992 0.8873\n+ 23 snp47 AFF B A 24/46/31 0.4554 0.4976 0.425\n+ 23 snp47 UNAFF B A 21/56/22 0.5657 0.4999 0.2316\n+ 23 snp49 ALL A B 54/88/58 0.44 0.4998 0.09091\n+ 23 snp49 AFF A B 24/47/30 0.4653 0.4982 0.5497\n+ 23 snp49 UNAFF A B 30/41/28 0.4141 0.4998 0.1068\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.het --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.het Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+ FID IID O(HOM) E(HOM) N(NM) F\n+ per0 per0 15 12.02 24 0.2488\n+ per1 per1 10 12.02 24 -0.1685\n+ per2 per2 15 12.02 24 0.2488\n+ per3 per3 10 12.02 24 -0.1685\n+ per4 per4 11 12.02 24 -0.08506\n+ per5 per5 9 12.02 24 -0.252\n+ per6 per6 13 12.02 24 0.08187\n+ per7 per7 10 12.02 24 -0.1685\n+ per8 per8 12 12.02 24 -0.001596\n+ per9 per9 6 12.02 24 -0.5024\n+ per10 per10 15 12.02 24 0.2488\n+ per11 per11 10 12.02 24 -0.1685\n+ per12 per12 14 12.02 24 0.1653\n+ per13 per13 10 12.02 24 -0.1685\n+ per14 per14 11 12.02 24 -0.08506\n+ per15 per15 14 12.02 24 0.1653\n+ per16 per16 7 12.02 24 -0.4189\n+ per17 per17 10 12.02 24 -0.1685\n+ per18 per18 10 12.02 24 -0.1685\n+ per19 per19 9 12.02 24 -0.252\n+ per20 per20 15 12.02 24 0.2488\n+ per21 per21 8 12.02 24 -0.3355\n+ per22 per22 5 12.02 24 -0.5859\n+ per23 per23 12 12.02 24 -0.001596\n+ per24 per24 12 12.02 24 -0.001596\n+ per25 per25 13 12.02 24 0.08187\n+ per26 per26 16 12.02 24 0.3323\n+ per27 per27 10 12.02 24 -0.1685\n+ per28 per28 11 12.02 24 -0.08506\n+ per29 per29 10 12.02 24 -0.1685\n+ per30 per30 9 12.02 24 -0.252\n+ per31 per31 11 12.02 24 -0.08506\n+ per32 per32 9 12.02 24 -0.252\n+ per33 per33 11 12.02 24 -0.08506\n+ per34 per34 13 12.02 24 0.08187\n+ per35 per35 10 12.02 24 -0.1685\n+ per36 per36 13 12.02 24 0.08187\n+ per37 per37 8 12.02 24 -0.3355\n+ per38 per38 12 12.02 24 -0.001596\n+ per39 per39 13 12.02 24 0.08187\n+ per40 per40 9 12.02 24 -0.252\n+ per41 per41 9 12.02 24 -0.252\n+ per42 per42 8 12.02 24 -0.3355\n+ per43 per43 15 12.02 24 0.2488\n+ per44 per44 9 12.02 24 -0.252\n+ per45 per45 11 12.02 24 -0.08506\n+ per46 per46 14 12.02 24 0.1653\n+ per47 per47 11 12.02 24 -0.08506\n+ per48 per48 9 12.02 24 -0.252\n+ per49 per49 17 12.02 24 0.4157\n+ per50 per50 12 12.02 24 -0.001596\n+ per51 per51 10 12.02 24 -0.1685\n+ per52 per52 11 12.02 24 -0.08506\n+ per53 per53 9 12.02 24 -0.252\n+ per54 per54 12 12.02 24 -0.001596\n+ per55 per55 15 12.02 24 0.2488\n+ per56 per56 9 12.02 '..b'er142 per142 12 12.02 24 -0.001596\n+ per143 per143 11 12.02 24 -0.08506\n+ per144 per144 7 12.02 24 -0.4189\n+ per145 per145 12 12.02 24 -0.001596\n+ per146 per146 12 12.02 24 -0.001596\n+ per147 per147 8 12.02 24 -0.3355\n+ per148 per148 19 12.02 24 0.5827\n+ per149 per149 13 12.02 24 0.08187\n+ per150 per150 15 12.02 24 0.2488\n+ per151 per151 9 12.02 24 -0.252\n+ per152 per152 15 12.02 24 0.2488\n+ per153 per153 16 12.02 24 0.3323\n+ per154 per154 9 12.02 24 -0.252\n+ per155 per155 13 12.02 24 0.08187\n+ per156 per156 12 12.02 24 -0.001596\n+ per157 per157 11 12.02 24 -0.08506\n+ per158 per158 12 12.02 24 -0.001596\n+ per159 per159 12 12.02 24 -0.001596\n+ per160 per160 10 12.02 24 -0.1685\n+ per161 per161 9 12.02 24 -0.252\n+ per162 per162 10 12.02 24 -0.1685\n+ per163 per163 8 12.02 24 -0.3355\n+ per164 per164 11 12.02 24 -0.08506\n+ per165 per165 12 12.02 24 -0.001596\n+ per166 per166 10 12.02 24 -0.1685\n+ per167 per167 11 12.02 24 -0.08506\n+ per168 per168 9 12.02 24 -0.252\n+ per169 per169 9 12.02 24 -0.252\n+ per170 per170 15 12.02 24 0.2488\n+ per171 per171 15 12.02 24 0.2488\n+ per172 per172 15 12.02 24 0.2488\n+ per173 per173 9 12.02 24 -0.252\n+ per174 per174 12 12.02 24 -0.001596\n+ per175 per175 10 12.02 24 -0.1685\n+ per176 per176 11 12.02 24 -0.08506\n+ per177 per177 11 12.02 24 -0.08506\n+ per178 per178 12 12.02 24 -0.001596\n+ per179 per179 10 12.02 24 -0.1685\n+ per180 per180 13 12.02 24 0.08187\n+ per181 per181 7 12.02 24 -0.4189\n+ per182 per182 12 12.02 24 -0.001596\n+ per183 per183 13 12.02 24 0.08187\n+ per184 per184 9 12.02 24 -0.252\n+ per185 per185 12 12.02 24 -0.001596\n+ per186 per186 12 12.02 24 -0.001596\n+ per187 per187 13 12.02 24 0.08187\n+ per188 per188 11 12.02 24 -0.08506\n+ per189 per189 13 12.02 24 0.08187\n+ per190 per190 9 12.02 24 -0.252\n+ per191 per191 15 12.02 24 0.2488\n+ per192 per192 10 12.02 24 -0.1685\n+ per193 per193 12 12.02 24 -0.001596\n+ per194 per194 12 12.02 24 -0.001596\n+ per195 per195 14 12.02 24 0.1653\n+ per196 per196 8 12.02 24 -0.3355\n+ per197 per197 11 12.02 24 -0.08506\n+ per198 per198 14 12.02 24 0.1653\n+ per199 per199 16 12.02 24 0.3323\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.imiss --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.imiss Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+ FID IID MISS_PHENO N_MISS N_GENO F_MISS\n+ per0 per0 N 0 50 0\n+ per1 per1 N 0 50 0\n+ per2 per2 N 0 50 0\n+ per3 per3 N 0 50 0\n+ per4 per4 N 0 50 0\n+ per5 per5 N 0 50 0\n+ per6 per6 N 0 50 0\n+ per7 per7 N 0 50 0\n+ per8 per8 N 0 50 0\n+ per9 per9 N 0 50 0\n+ per10 per10 N 0 50 0\n+ per11 per11 N 0 50 0\n+ per12 per12 N 0 50 0\n+ per13 per13 N 0 50 0\n+ per14 per14 N 0 50 0\n+ per15 per15 N 0 50 0\n+ per16 per16 N 0 50 0\n+ per17 per17 N 0 50 0\n+ per18 per18 N 0 50 0\n+ per19 per19 N 0 50 0\n+ per20 per20 N 0 50 0\n+ per21 per21 N 0 50 0\n+ per22 per22 N 0 50 0\n+ per23 per23 N 0 50 0\n+ per24 per24 N 0 50 0\n+ per25 per25 N 0 50 0\n+ per26 per26 N 0 50 0\n+ per27 per27 N 0 50 0\n+ per28 per28 N 0 50 0\n+ per29 per29 N 0 50 0\n+ per30 per30 N 0 50 0\n+ per31 per31 N 0 50 0\n+ per32 per32 N 0 50 0\n+ per33 per33 N 0 50 0\n+ per34 per34 N 0 50 0\n+ per35 per35 N 0 50 0\n+ per36 per36 N 0 50 0\n+ per37 per37 N 0 50 0\n+ per38 per38 N 0 50 0\n+ per39 per39 N 0 50 0\n+ per40 per40 N 0 50 0\n+ per41 per41 N 0 50 0\n+ per42 per42 N 0 50 0\n+ per43 per43 N 0 50 0\n+ per44 per44 N 0 50 0\n+ per45 per45 N 0 50 0\n+ per46 per46 N 0 50 0\n+ per47 per47 N 0 50 0\n+ per48 per48 N 0 50 0\n+ per49 per49 N 0 50 0\n+ per50 per50 N 0 50 0\n+ per51 per51 N 0 50 0\n+ per52 per52 N 0 50 0\n+ per53 per53 N 0 50 0\n+ per54 per54 N 0 50 0\n+ per55 per55 N 0 50 0\n+ per56 per56 N 0 50 0\n+ per57 per57 N 0 50 0\n+ per58 per58 N 0 50 0\n+ per59 per59 N 0 50 0\n+ per60 per60 N 0 50 0\n+ per61 per61 N 0 50 0\n+ per62 per62 N 0 50 0\n+ per63 per63 N 0 50 0\n+ per64 per64 N 0 50 0\n+ per65 per65 N 0 50 0\n+ per66 per66 N 0 50 0\n+ per67 per67 N 0 50 0\n+ per68 per68 N 0 50 0\n+ per69 per69 N 0 50 0\n+ per70 per70 N 0 50 0\n+ per71 per71 '..b' N 0 50 0\n+ per128 per128 N 0 50 0\n+ per129 per129 N 0 50 0\n+ per130 per130 N 0 50 0\n+ per131 per131 N 0 50 0\n+ per132 per132 N 0 50 0\n+ per133 per133 N 0 50 0\n+ per134 per134 N 0 50 0\n+ per135 per135 N 0 50 0\n+ per136 per136 N 0 50 0\n+ per137 per137 N 0 50 0\n+ per138 per138 N 0 50 0\n+ per139 per139 N 0 50 0\n+ per140 per140 N 0 50 0\n+ per141 per141 N 0 50 0\n+ per142 per142 N 0 50 0\n+ per143 per143 N 0 50 0\n+ per144 per144 N 0 50 0\n+ per145 per145 N 0 50 0\n+ per146 per146 N 0 50 0\n+ per147 per147 N 0 50 0\n+ per148 per148 N 0 50 0\n+ per149 per149 N 0 50 0\n+ per150 per150 N 0 50 0\n+ per151 per151 N 0 50 0\n+ per152 per152 N 0 50 0\n+ per153 per153 N 0 50 0\n+ per154 per154 N 0 50 0\n+ per155 per155 N 0 50 0\n+ per156 per156 N 0 50 0\n+ per157 per157 N 0 50 0\n+ per158 per158 N 0 50 0\n+ per159 per159 N 0 50 0\n+ per160 per160 N 0 50 0\n+ per161 per161 N 0 50 0\n+ per162 per162 N 0 50 0\n+ per163 per163 N 0 50 0\n+ per164 per164 N 0 50 0\n+ per165 per165 N 0 50 0\n+ per166 per166 N 0 50 0\n+ per167 per167 N 0 50 0\n+ per168 per168 N 0 50 0\n+ per169 per169 N 0 50 0\n+ per170 per170 N 0 50 0\n+ per171 per171 N 0 50 0\n+ per172 per172 N 0 50 0\n+ per173 per173 N 0 50 0\n+ per174 per174 N 0 50 0\n+ per175 per175 N 0 50 0\n+ per176 per176 N 0 50 0\n+ per177 per177 N 0 50 0\n+ per178 per178 N 0 50 0\n+ per179 per179 N 0 50 0\n+ per180 per180 N 0 50 0\n+ per181 per181 N 0 50 0\n+ per182 per182 N 0 50 0\n+ per183 per183 N 0 50 0\n+ per184 per184 N 0 50 0\n+ per185 per185 N 0 50 0\n+ per186 per186 N 0 50 0\n+ per187 per187 N 0 50 0\n+ per188 per188 N 0 50 0\n+ per189 per189 N 0 50 0\n+ per190 per190 N 0 50 0\n+ per191 per191 N 0 50 0\n+ per192 per192 N 0 50 0\n+ per193 per193 N 0 50 0\n+ per194 per194 N 0 50 0\n+ per195 per195 N 0 50 0\n+ per196 per196 N 0 50 0\n+ per197 per197 N 0 50 0\n+ per198 per198 N 0 50 0\n+ per199 per199 N 0 50 0\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.lmiss --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.lmiss Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ + CHR SNP N_MISS N_GENO F_MISS + 1 snp0 0 200 0 + 1 snp1 0 200 0 + 1 snp2 0 200 0 + 1 snp3 0 200 0 + 1 snp4 0 200 0 + 1 snp5 0 200 0 + 1 snp6 0 200 0 + 1 snp7 0 200 0 + 1 snp8 0 200 0 + 1 snp9 0 200 0 + 1 snp10 0 200 0 + 1 snp11 0 200 0 + 1 snp12 0 200 0 + 1 snp13 0 200 0 + 1 snp14 0 200 0 + 1 snp15 0 200 0 + 1 snp16 0 200 0 + 1 snp39 0 200 0 + 1 snp40 0 200 0 + 1 snp41 0 200 0 + 1 snp42 0 200 0 + 1 snp44 0 200 0 + 1 snp46 0 200 0 + 1 snp48 0 200 0 + 23 snp17 0 200 0 + 23 snp18 0 200 0 + 23 snp19 0 200 0 + 23 snp20 0 200 0 + 23 snp21 0 200 0 + 23 snp22 0 200 0 + 23 snp23 0 200 0 + 23 snp24 0 200 0 + 23 snp25 0 200 0 + 23 snp26 0 200 0 + 23 snp27 0 200 0 + 23 snp28 0 200 0 + 23 snp29 0 200 0 + 23 snp30 0 200 0 + 23 snp31 0 200 0 + 23 snp32 0 200 0 + 23 snp33 0 200 0 + 23 snp34 0 200 0 + 23 snp35 0 200 0 + 23 snp36 0 200 0 + 23 snp37 0 200 0 + 23 snp38 0 200 0 + 23 snp43 0 200 0 + 23 snp45 0 200 0 + 23 snp47 0 200 0 + 23 snp49 0 200 0 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.map Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,300 @@ +1 snp0 0 0 +1 snp1 0 1 +1 snp2 0 2 +1 snp3 0 3 +1 snp4 0 4 +1 snp5 0 5 +1 snp6 0 6 +1 snp7 0 7 +1 snp8 0 8 +1 snp9 0 9 +1 snp10 0 10 +1 snp11 0 11 +1 snp12 0 12 +1 snp13 0 13 +1 snp14 0 14 +1 snp15 0 15 +1 snp16 0 16 +1 snp17 0 17 +1 snp18 0 18 +1 snp19 0 19 +1 snp20 0 20 +1 snp21 0 21 +1 snp22 0 22 +1 snp23 0 23 +1 snp24 0 24 +1 snp25 0 25 +1 snp26 0 26 +1 snp27 0 27 +1 snp28 0 28 +1 snp29 0 29 +1 snp30 0 30 +1 snp31 0 31 +1 snp32 0 32 +1 snp33 0 33 +1 snp34 0 34 +1 snp35 0 35 +1 snp36 0 36 +1 snp37 0 37 +1 snp38 0 38 +1 snp39 0 39 +1 snp40 0 40 +1 snp41 0 41 +1 snp42 0 42 +1 snp43 0 43 +1 snp44 0 44 +1 snp45 0 45 +1 snp46 0 46 +1 snp47 0 47 +1 snp48 0 48 +1 snp49 0 49 +1 snp50 0 50 +1 snp51 0 51 +1 snp52 0 52 +1 snp53 0 53 +1 snp54 0 54 +1 snp55 0 55 +1 snp56 0 56 +1 snp57 0 57 +1 snp58 0 58 +1 snp59 0 59 +1 snp60 0 60 +1 snp61 0 61 +1 snp62 0 62 +1 snp63 0 63 +1 snp64 0 64 +1 snp65 0 65 +1 snp66 0 66 +1 snp67 0 67 +1 snp68 0 68 +1 snp69 0 69 +1 snp70 0 70 +1 snp71 0 71 +1 snp72 0 72 +1 snp73 0 73 +1 snp74 0 74 +1 snp75 0 75 +1 snp76 0 76 +1 snp77 0 77 +1 snp78 0 78 +1 snp79 0 79 +1 snp80 0 80 +1 snp81 0 81 +1 snp82 0 82 +1 snp83 0 83 +1 snp84 0 84 +1 snp85 0 85 +1 snp86 0 86 +1 snp87 0 87 +1 snp88 0 88 +1 snp89 0 89 +1 snp90 0 90 +1 snp91 0 91 +1 snp92 0 92 +1 snp93 0 93 +1 snp94 0 94 +1 snp95 0 95 +1 snp96 0 96 +1 snp97 0 97 +1 snp98 0 98 +1 snp99 0 99 +1 snp100 0 100 +1 snp101 0 101 +1 snp102 0 102 +1 snp103 0 103 +1 snp104 0 104 +1 snp105 0 105 +1 snp106 0 106 +1 snp107 0 107 +1 snp108 0 108 +1 snp109 0 109 +1 snp110 0 110 +1 snp111 0 111 +1 snp112 0 112 +1 snp113 0 113 +1 snp114 0 114 +1 snp115 0 115 +1 snp116 0 116 +1 snp117 0 117 +1 snp118 0 118 +1 snp119 0 119 +1 snp120 0 120 +1 snp121 0 121 +1 snp122 0 122 +1 snp123 0 123 +1 snp124 0 124 +1 snp125 0 125 +1 snp126 0 126 +1 snp127 0 127 +1 snp128 0 128 +1 snp129 0 129 +1 snp130 0 130 +1 snp131 0 131 +1 snp132 0 132 +1 snp133 0 133 +1 snp134 0 134 +1 snp135 0 135 +1 snp136 0 136 +1 snp137 0 137 +1 snp138 0 138 +1 snp139 0 139 +1 snp140 0 140 +1 snp141 0 141 +1 snp142 0 142 +1 snp143 0 143 +1 snp144 0 144 +1 snp145 0 145 +1 snp146 0 146 +1 snp147 0 147 +1 snp148 0 148 +1 snp149 0 149 +1 snp150 0 150 +1 snp151 0 151 +1 snp152 0 152 +1 snp153 0 153 +1 snp154 0 154 +1 snp155 0 155 +1 snp156 0 156 +1 snp157 0 157 +1 snp158 0 158 +1 snp159 0 159 +1 snp160 0 160 +1 snp161 0 161 +1 snp162 0 162 +1 snp163 0 163 +1 snp164 0 164 +1 snp165 0 165 +1 snp166 0 166 +1 snp167 0 167 +1 snp168 0 168 +1 snp169 0 169 +1 snp170 0 170 +1 snp171 0 171 +1 snp172 0 172 +1 snp173 0 173 +1 snp174 0 174 +1 snp175 0 175 +1 snp176 0 176 +1 snp177 0 177 +1 snp178 0 178 +1 snp179 0 179 +1 snp180 0 180 +1 snp181 0 181 +1 snp182 0 182 +1 snp183 0 183 +1 snp184 0 184 +1 snp185 0 185 +1 snp186 0 186 +1 snp187 0 187 +1 snp188 0 188 +1 snp189 0 189 +1 snp190 0 190 +1 snp191 0 191 +1 snp192 0 192 +1 snp193 0 193 +1 snp194 0 194 +1 snp195 0 195 +1 snp196 0 196 +1 snp197 0 197 +1 snp198 0 198 +1 snp199 0 199 +1 snp200 0 200 +1 snp201 0 201 +1 snp202 0 202 +1 snp203 0 203 +1 snp204 0 204 +1 snp205 0 205 +1 snp206 0 206 +1 snp207 0 207 +1 snp208 0 208 +1 snp209 0 209 +1 snp210 0 210 +1 snp211 0 211 +1 snp212 0 212 +1 snp213 0 213 +1 snp214 0 214 +1 snp215 0 215 +1 snp216 0 216 +1 snp217 0 217 +1 snp218 0 218 +1 snp219 0 219 +1 snp220 0 220 +1 snp221 0 221 +1 snp222 0 222 +1 snp223 0 223 +1 snp224 0 224 +1 snp225 0 225 +1 snp226 0 226 +1 snp227 0 227 +1 snp228 0 228 +1 snp229 0 229 +1 snp230 0 230 +1 snp231 0 231 +1 snp232 0 232 +1 snp233 0 233 +1 snp234 0 234 +1 snp235 0 235 +1 snp236 0 236 +1 snp237 0 237 +1 snp238 0 238 +1 snp239 0 239 +1 snp240 0 240 +1 snp241 0 241 +1 snp242 0 242 +1 snp243 0 243 +1 snp244 0 244 +1 snp245 0 245 +1 snp246 0 246 +1 snp247 0 247 +1 snp248 0 248 +1 snp249 0 249 +1 snp250 0 250 +1 snp251 0 251 +1 snp252 0 252 +1 snp253 0 253 +1 snp254 0 254 +1 snp255 0 255 +1 snp256 0 256 +1 snp257 0 257 +1 snp258 0 258 +1 snp259 0 259 +1 snp260 0 260 +1 snp261 0 261 +1 snp262 0 262 +1 snp263 0 263 +1 snp264 0 264 +1 snp265 0 265 +1 snp266 0 266 +1 snp267 0 267 +1 snp268 0 268 +1 snp269 0 269 +1 snp270 0 270 +1 snp271 0 271 +1 snp272 0 272 +1 snp273 0 273 +1 snp274 0 274 +1 snp275 0 275 +1 snp276 0 276 +1 snp277 0 277 +1 snp278 0 278 +1 snp279 0 279 +1 snp280 0 280 +1 snp281 0 281 +1 snp282 0 282 +1 snp283 0 283 +1 snp284 0 284 +1 snp285 0 285 +1 snp286 0 286 +1 snp287 0 287 +1 snp288 0 288 +1 snp289 0 289 +1 snp290 0 290 +1 snp291 0 291 +1 snp292 0 292 +1 snp293 0 293 +1 snp294 0 294 +1 snp295 0 295 +1 snp296 0 296 +1 snp297 0 297 +1 snp298 0 298 +1 snp299 0 299 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.ped Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,500 @@\n+per0 per0 0 0 2 1 0 0 B A 0 0 0 0 0 0 B B A B 0 0 A A A B B B 0 0 B A 0 0 0 0 A B 0 0 0 0 0 0 A B B B B B 0 0 0 0 0 0 A B 0 0 0 0 0 0 0 0 0 0 0 0 A B A A 0 0 0 0 0 0 A A 0 0 0 0 0 0 A B A B 0 0 A B A B 0 0 0 0 B B B A A B B B A A B A A A A B A B B A B A A B B A B B A B B A A A B A B B B B A A A A A B B A B B B A B A A B A A A B B A A B A B B A A B A A B A A B B A A A B B A A A A B A A A A B A B B A A A B A A B A B A A A B B A A A A B A B B B B B B B B A B A B B B A A A B B A B B B B B B A A A A B B B A A A B A A B B A B B B A B A B A A B A B A A A B B B B A A B B B B B A A B B A A A A A A B A A A A B A B A A B A A B A A B A A A A B A A B A A B B B A A B B B B A B B A A A A A B B B B A B A A B B B A B A A A B B B A A B B B A A A B A B A B B A A A A B B A A A B B B B B A A A A A B B A A A B A B B B B A A A A B B A B A B B A B B B B B B B A A B A B B A B A A A A B B A A B B A B B B A A A A A A B A A B B B B B A A A B A B A A A A B B A B A A A B A B A B A B A A A B A B B B A B A B B B A B A A B A A A A A A B A A A A A A B B B B B B A A B B B A B B A A B A B B B B B A A B B B B A A B B B B A B B A A B B A B B B B A B B A B B B A A A A B B B A B A B B B B A B B B B A B A A A B A A A A B B A A B A A A B B\n+per1 per1 0 0 2 2 0 0 B B 0 0 A B 0 0 0 0 0 0 B A B A A B A B A B 0 0 0 0 0 0 0 0 0 0 A A B A 0 0 0 0 B A 0 0 0 0 A B 0 0 B A 0 0 0 0 0 0 0 0 B A A B A B B A B A 0 0 A B 0 0 A A 0 0 0 0 A B 0 0 0 0 B B 0 0 B A A A 0 0 A A B A B A B A B B A A A A A A B A A A B A B B A B B A A A B A B A B A A A A A A B B A A B B A A A A B B B A B B B A B A B B B A B A A A A A A A A B A B A A B B A B A B B A B A B B B B A B B A B A B A A B B B A B B A B B B B A A A A B A A B A B A B A A B A A A B B A A B A A A B A B B A A B A A A B A B A B B B B B A A B A B A B A B A A A B A A A A B A A A A B B A A B A A B B B A B B A A A A A B B B B B A B B A A A B B A A A A A A B B B B B B A B A B B A B A A A B B B B A B A A A A A B B B A A B A B B A A A B B A A B B B A A A B B B B B A A A A B A B B A B A A A A B B A B A B B B B A B B B B B A A A B A B B A B B B B B B B A A A B B B A A A B A B B B B A B A A A B B B B B B A A B B A A B A A B A B B B A A A B A B B B A B A A B A A B A B B A A B A A A A A B A A A B A B B A A A A A A A A B A A A A A B B A B B A A A B B A B A B A A B A A A A A B B B B A A B A A B B B B A A B A B B A A B B B A B A A A B A A B A B B A A A B A A A A B B A A B B A B B B B B B A A A A B A A A A A A B B B B A A\n+per2 per2 0 0 2 1 A B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 B B 0 0 0 0 0 0 A A 0 0 0 0 0 0 0 0 A B A A A A 0 0 0 0 A B A B 0 0 0 0 0 0 0 0 0 0 B A 0 0 0 0 0 0 B A B A A B B A 0 0 A A A A 0 0 0 0 0 0 A B 0 0 0 0 A B 0 0 B B B A A A B A B A A B A B B A B B A A B B B A A B B B B A A A B A B A A A A A A B B B A B B B B A B B A A B B B A A B A A B B A B A A B A A B B A B A B A B B B B B B A B A B B B B B B B B B B B B B A A A B B A B A A B A B B A B B A A A A B A B A B A A A A B A B A A A A A A A A A B B A B B A A A B A A B B B B A A A B B A B B B A B B B B B B B A B B B A B B A B A A B A A B A B B B B A B A B A A A B B A A B B A A A A B B A A A B A A B A A A B B B B A A A B A A A B A A B A B A A B A B A B A A B B A A B A A B B A B A A A B A A B A A B B B B A A A B A B B A A A A B A B B A B B A A A A A B A A B A A B A B A A B B A A B B B A B A A B A A B A B A B B A B A A A A A A B B B B A A B B A A B B A A A B B B A B B A A A B A A B B B A A B B B A B B B B B A B B B B A B B A B B B B A A B B A B A A A B A A B B A B B B B B A A B A B A A B A A B B B A B B A B B B A B B B A A A B B B B B A B B B A A A B A A B B A B A B B B B B A A B A B B B A A B A B B B B A A B A A A B B A A B A B A B A A B B B A B A B B\n+per3 per3 0 0 2 1 0 0 0 0 B A A B 0 0 0 0 0 0 A A 0 0 A B 0 0 A B 0 0 A A B A 0 0 B A 0 0 0 0 A B 0 0 0 0 A A A A 0 0 B B B A B B A B A B 0 0 0 0 0 0 A B 0 0 0 0 0 0 A B 0 0 B B 0 0 0 0 0 0 0 0 B B 0 0 0 0 0 0 A B 0 0 A B A A B B B A A A A B A A A A B A A B B A B B A B B A A A A A B A B A A B A A A A A A A A A A B B A A A'..b'B B A B A B A A A B B A B B B B A A B B B B A B A B B B A B B B B B B A A B A B A B A B A A A B A B A A A B A B A A A A B B B B B B A B B B A A B A A B A B A A B A B B B A A A B A B B B A A B A A A A B A B B B A B A B B A B B B A A A A A A B B A B B B A B B B B B B A A A A A A A A A A A A B B B A A B A B A B A B A B A A B A A A\n+per497 per497 0 0 2 2 A B B A B B B B A A A B B B A A A A A B A B B B A A B A B A B B A A A A B B A B A A B B A B B B A A A B B A B B A A B B A A B B B B A A B B B B B A A A B A A A B A A B A B A A A B A A A A B B A A A A A B B A B A A A A A B B B B A A B A A B B B B B A B A A B A B A A A B A A B B A A A B A A B B B B B A A A A A B B B B B A A B A A A B B A A A B B B B A A A B B B A B A A B A B A B B B B B A A B B A B A A B B B A B B A B A A B B A B A B B A A A B B B A A A A B A B A A A A A A B B B B B A A A A B A B A B B B B A A B A B B A B A B A B A A A B A B A A A B A B A A A B B A A A B A B A B B A B A B B A B A B B A B B A A A A B A A A A B B B B A A B B A B A B B A A B A A B A B A A B A A B A B A A B B A B A B B B A B B B B A A A A A A B A A A B B B B B A B A A B B B A A B A A A A B B B A A B A B A B A A A B B B A A B A A B B A A A B A B B A B B A B A B A A A B A B B B A A B B B B A A A A B B A A B A B A A A B B A B A B A A A B A B A B B B A A A A A B A A A B A A A B B B A B A B A B A A B A B A B B B A A A A B A A B B A B B A A B B A A A B A A A B A B B A A B A A B A B B A B B A A A A B B B A B B A A B B B A B B A B A B B A A A B A A A A B B B B B A B B B B A B B A A A A A A B B B A B B B B A A B\n+per498 per498 0 0 2 1 B B B B B A A B A B A B A B B A A A A B B B B B B A B B B A A B B B B A B A B B A A B A B B A A A A A A A A A A A A A B B B B A A B A A A A B B B A A B B A A A B A A B B B A B A B B B A B B A A A B A A B B B B B B A B B A B B B B B A A B B B A B A B B B A B B B A B B A A A B B A B B B A A B B A A A A B B A B B B A A B A A B A B B B B B A A B A A A A A A A A B A B A B B B B A A B A A A B A A B B B A A A B B B A A A B B B B A A B B B B A B A B A B A A B A A A B B A A A B B A B A A B A B B A B A B B B A B A A A A A A B A A A A A B A A A A A B A A B B B B A A A A A B B B B A A B B A A B A A A A B A B B B A A A B B B B B A B A B A B B B A B B A B A A A B B B B B B B B B B B A A B A A B B B B A B A A A A B B A A B B B A A A B B A A A B B A A A B B B B B B A A A B A B B A B B A A A A A B A A A A A A A B A B B A A A A A B A B B A A A B B A A A B A A B B A A B B A B B B A B A B B B B A A A B A A B A B B B B A A A A A B B A B B A B B A B A B B B A A A B B A A B B A A B A B B A A A B A B A A B A B A B B B A A B B B A A A A A A B B A B A A A B A B B A B B B B A A B B A B A A A A B B B A B B B A A B A B A B A A B A B A B A B B B A A B A B A A B A B B A B A B B A B B A A A B A A A B A A B A B B\n+per499 per499 0 0 2 1 A B B A B A A A A B B B B B A A B A A B B B A B A A B A B B A A A A B B B A A A A A A A B B B B A B B B B A A A A B A A B A B B A A A B B A B A A A B B A A A B B A A A A B A A A B A A A A B A A B B A A B B B B A B B B A B B A B B A A A A A B B B A B B B A A A A A A A B B A B B B B B A A A B B A B B B B B B A A B A A A A B B A A B B B A A A B B A B A B A A B B B B A A B B B A A B A B B B A A B A A B B A A B A A A A A A B A A A B B B B A B A A A A A B B A B A B B B A A B A B B A B B A A B A B A B A B A B B A A A A A B B A A A A A A A B A A B A A B B A B B B B B B B B A A B B A B A A A A B A A A A B B A A B A A A B B B A B A A B B B A B B A A A A A A A A A A A B B B A A A A A B A B B B B B A B A A B A A B A A B B B A B A A A A A B B B B B A A B A B B A B A A B A B A A B A A A A B A B A B B A B B A B A A B A A A A A B A B A B B A B B A A A B B A B A A A A B A A A A A B A B A B B A A B B B B A A A B B A B B B A A B B B B A A B B A B A B A A A B B B A A B B A A A B B B B B B A B A B A A A A B A A B B A B B B B B B B A B B A A A B B A A A B B B A A A B A B A B B B B B A A B A B B A A B A A A B A B A B A A A A B B B A B B A A B B A A A A A A A A A B A A B A A A A B A B A A A B A A B A A A\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/out.sexcheck --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.sexcheck Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+ FID IID PEDSEX SNPSEX STATUS F YCOUNT\n+ per0 per0 2 2 OK -0.00203 0\n+ per1 per1 2 2 OK -0.3874 0\n+ per2 per2 2 2 OK -0.3874 0\n+ per3 per3 2 2 OK -0.2333 0\n+ per4 per4 2 2 OK -0.00203 0\n+ per5 per5 2 2 OK -0.00203 0\n+ per6 per6 2 2 OK -0.07911 0\n+ per7 per7 2 2 OK -0.00203 0\n+ per8 per8 2 0 PROBLEM 0.2292 0\n+ per9 per9 2 2 OK 0.07505 0\n+ per10 per10 2 2 OK -0.07911 0\n+ per11 per11 2 2 OK 0.1521 0\n+ per12 per12 2 2 OK -0.00203 0\n+ per13 per13 2 2 OK -0.00203 0\n+ per14 per14 2 2 OK -0.2333 0\n+ per15 per15 2 2 OK -0.00203 0\n+ per16 per16 2 0 PROBLEM 0.2292 0\n+ per17 per17 2 2 OK -0.07911 0\n+ per18 per18 2 2 OK -0.07911 0\n+ per19 per19 2 2 OK -0.1562 0\n+ per20 per20 2 2 OK 0.07505 0\n+ per21 per21 2 2 OK 0.07505 0\n+ per22 per22 2 2 OK 0.07505 0\n+ per23 per23 2 2 OK 0.1521 0\n+ per24 per24 2 2 OK -0.2333 0\n+ per25 per25 2 2 OK -0.4645 0\n+ per26 per26 2 2 OK 0.1521 0\n+ per27 per27 2 2 OK 0.07505 0\n+ per28 per28 2 2 OK 0.1521 0\n+ per29 per29 2 2 OK -0.1562 0\n+ per30 per30 2 2 OK -0.00203 0\n+ per31 per31 2 0 PROBLEM 0.2292 0\n+ per32 per32 2 2 OK 0.07505 0\n+ per33 per33 2 2 OK -0.00203 0\n+ per34 per34 2 2 OK -0.00203 0\n+ per35 per35 2 0 PROBLEM 0.2292 0\n+ per36 per36 2 2 OK 0.07505 0\n+ per37 per37 2 2 OK 0.1521 0\n+ per38 per38 2 2 OK -0.07911 0\n+ per39 per39 2 2 OK 0.07505 0\n+ per40 per40 2 2 OK -0.2333 0\n+ per41 per41 2 2 OK -0.07911 0\n+ per42 per42 2 0 PROBLEM 0.4604 0\n+ per43 per43 2 2 OK -0.5416 0\n+ per44 per44 2 2 OK -0.00203 0\n+ per45 per45 2 0 PROBLEM 0.2292 0\n+ per46 per46 2 2 OK -0.1562 0\n+ per47 per47 2 2 OK 0.1521 0\n+ per48 per48 2 2 OK 0.1521 0\n+ per49 per49 2 2 OK 0.07505 0\n+ '..b' 0.07505 0\n+ per149 per149 2 2 OK 0.1521 0\n+ per150 per150 2 2 OK -0.2333 0\n+ per151 per151 2 2 OK -0.2333 0\n+ per152 per152 2 2 OK 0.1521 0\n+ per153 per153 2 2 OK -0.1562 0\n+ per154 per154 2 2 OK 0.1521 0\n+ per155 per155 2 2 OK -0.07911 0\n+ per156 per156 2 2 OK -0.1562 0\n+ per157 per157 2 2 OK -0.2333 0\n+ per158 per158 2 2 OK 0.07505 0\n+ per159 per159 2 0 PROBLEM 0.2292 0\n+ per160 per160 2 2 OK -0.00203 0\n+ per161 per161 2 0 PROBLEM 0.2292 0\n+ per162 per162 2 2 OK -0.00203 0\n+ per163 per163 2 2 OK -0.1562 0\n+ per164 per164 2 2 OK -0.07911 0\n+ per165 per165 2 0 PROBLEM 0.2292 0\n+ per166 per166 2 0 PROBLEM 0.3834 0\n+ per167 per167 2 0 PROBLEM 0.3063 0\n+ per168 per168 2 2 OK 0.07505 0\n+ per169 per169 2 2 OK 0.1521 0\n+ per170 per170 2 2 OK -0.00203 0\n+ per171 per171 2 2 OK 0.07505 0\n+ per172 per172 2 2 OK -0.07911 0\n+ per173 per173 2 0 PROBLEM 0.5375 0\n+ per174 per174 2 2 OK -0.00203 0\n+ per175 per175 2 2 OK 0.1521 0\n+ per176 per176 2 0 PROBLEM 0.3834 0\n+ per177 per177 2 2 OK -0.00203 0\n+ per178 per178 2 0 PROBLEM 0.3834 0\n+ per179 per179 2 2 OK -0.3103 0\n+ per180 per180 2 0 PROBLEM 0.3063 0\n+ per181 per181 2 0 PROBLEM 0.3063 0\n+ per182 per182 2 2 OK -0.00203 0\n+ per183 per183 2 2 OK -0.00203 0\n+ per184 per184 2 2 OK -0.00203 0\n+ per185 per185 2 2 OK 0.07505 0\n+ per186 per186 2 0 PROBLEM 0.2292 0\n+ per187 per187 2 0 PROBLEM 0.3063 0\n+ per188 per188 2 2 OK -0.1562 0\n+ per189 per189 2 2 OK 0.1521 0\n+ per190 per190 2 2 OK -0.07911 0\n+ per191 per191 2 2 OK -0.00203 0\n+ per192 per192 2 2 OK -0.00203 0\n+ per193 per193 2 2 OK -0.3874 0\n+ per194 per194 2 2 OK -0.07911 0\n+ per195 per195 2 2 OK -0.00203 0\n+ per196 per196 2 2 OK -0.07911 0\n+ per197 per197 2 2 OK -0.07911 0\n+ per198 per198 2 2 OK -0.2333 0\n+ per199 per199 2 2 OK -0.07911 0\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.bed |
| b |
| Binary file test-data/plink.bed has changed |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.bim Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,50 @@ +1 snp0 0 0 A B +1 snp1 0 1 A B +1 snp2 0 2 A B +1 snp3 0 3 B A +1 snp4 0 4 B A +1 snp5 0 5 B A +1 snp6 0 6 A B +1 snp7 0 7 A B +1 snp8 0 8 B A +1 snp9 0 9 A B +1 snp10 0 10 B A +1 snp11 0 11 B A +1 snp12 0 12 B A +1 snp13 0 13 A B +1 snp14 0 14 B A +1 snp15 0 15 A B +1 snp16 0 16 A B +1 snp17 0 17 B A +1 snp18 0 18 B A +1 snp19 0 19 A B +1 snp20 0 20 A B +1 snp21 0 21 A B +1 snp22 0 22 A B +1 snp23 0 23 B A +1 snp24 0 24 A B +1 snp25 0 25 A B +1 snp26 0 26 B A +1 snp27 0 27 A B +1 snp28 0 28 B A +1 snp29 0 29 B A +1 snp30 0 30 A B +1 snp31 0 31 B A +1 snp32 0 32 B A +1 snp33 0 33 A B +1 snp34 0 34 B A +1 snp35 0 35 B A +1 snp36 0 36 A B +1 snp37 0 37 A B +1 snp38 0 38 B A +1 snp39 0 39 B A +1 snp40 0 40 B A +1 snp41 0 41 B A +1 snp42 0 42 B A +1 snp43 0 43 A B +1 snp44 0 44 A B +1 snp45 0 45 A B +1 snp46 0 46 A B +1 snp47 0 47 B A +1 snp48 0 48 B A +1 snp49 0 49 A B |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.cluster1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.cluster1 Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +SOL-0 per0_per0(1) per82_per82(1) per133_per133(2) per51_per51(1) per128_per128(2) per142_per142(1) per1_per1(2) per179_per179(1) per143_per143(1) per132_per132(2) per38_per38(2) per56_per56(2) per73_per73(1) per193_per193(2) per22_per22(2) per135_per135(1) per161_per161(1) per103_per103(1) per4_per4(1) per30_per30(2) per69_per69(1) per74_per74(2) per119_per119(2) per16_per16(2) per40_per40(1) per144_per144(2) per19_per19(2) per124_per124(1) per196_per196(1) per53_per53(1) per121_per121(1) per151_per151(2) per141_per141(1) per153_per153(2) per41_per41(1) per59_per59(1) per106_per106(2) per63_per63(1) per71_per71(2) per191_per191(1) per31_per31(2) per163_per163(1) per177_per177(2) per42_per42(2) per70_per70(2) per84_per84(1) per137_per137(1) per48_per48(1) per94_per94(2) per127_per127(1) per147_per147(2) per114_per114(2) per178_per178(1) per6_per6(2) per35_per35(1) per24_per24(1) per33_per33(1) per108_per108(2) per44_per44(2) per138_per138(1) per65_per65(2) per104_per104(1) per120_per120(2) per113_per113(1) per129_per129(2) per184_per184(1) per86_per86(1) per92_per92(2) per190_per190(1) per185_per185(1) per93_per93(1) per145_per145(2) per187_per187(1) per25_per25(1) per43_per43(2) per123_per123(1) per85_per85(2) per54_per54(2) per78_per78(1) per110_per110(1) per46_per46(2) per83_per83(1) per95_per95(2) per58_per58(2) per2_per2(1) per27_per27(2) per64_per64(1) per12_per12(1) per21_per21(2) per61_per61(2) per136_per136(1) per100_per100(2) per105_per105(2) per118_per118(2) per150_per150(1) per3_per3(1) per164_per164(2) per198_per198(1) per9_per9(1) per175_per175(2) per45_per45(2) per11_per11(2) per183_per183(1) per182_per182(1) per29_per29(2) per192_per192(1) per165_per165(2) per160_per160(2) per166_per166(1) per162_per162(2) per181_per181(1) per7_per7(2) per172_per172(1) per176_per176(2) per34_per34(1) per60_per60(2) per188_per188(1) per107_per107(2) per14_per14(2) per168_per168(1) per117_per117(2) per96_per96(2) per15_per15(1) per81_per81(2) per171_per171(1) per36_per36(2) per115_per115(1) per68_per68(2) per134_per134(1) per146_per146(1) per148_per148(2) per18_per18(1) per28_per28(2) per111_per111(1) per158_per158(2) per140_per140(1) per50_per50(2) per156_per156(1) per194_per194(2) per79_per79(2) per157_per157(1) per17_per17(2) per169_per169(1) per99_per99(2) per122_per122(2) per20_per20(2) per173_per173(1) per47_per47(2) per101_per101(2) per130_per130(2) per197_per197(1) per152_per152(1) per102_per102(1) per8_per8(1) per13_per13(2) per125_per125(1) per154_per154(2) per155_per155(1) per10_per10(1) per89_per89(2) per57_per57(2) per88_per88(1) per170_per170(2) per5_per5(1) per76_per76(2) per23_per23(2) per52_per52(2) per62_per62(2) per159_per159(1) per87_per87(2) per139_per139(1) per32_per32(2) per67_per67(1) per91_per91(1) per112_per112(2) per126_per126(2) per55_per55(1) per66_per66(2) per109_per109(1) per97_per97(1) per189_per189(2) per37_per37(2) per180_per180(1) per75_per75(1) per77_per77(2) per174_per174(1) per26_per26(2) per80_per80(1) per116_per116(1) per131_per131(2) per167_per167(1) per186_per186(2) per39_per39(1) per149_per149(2) per49_per49(1) per199_per199(2) per72_per72(2) per90_per90(2) per195_per195(1) per98_per98(2) |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.cluster2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.cluster2 Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,200 @@ +per0 per0 0 +per1 per1 0 +per2 per2 0 +per3 per3 0 +per4 per4 0 +per5 per5 0 +per6 per6 0 +per7 per7 0 +per8 per8 0 +per9 per9 0 +per10 per10 0 +per11 per11 0 +per12 per12 0 +per13 per13 0 +per14 per14 0 +per15 per15 0 +per16 per16 0 +per17 per17 0 +per18 per18 0 +per19 per19 0 +per20 per20 0 +per21 per21 0 +per22 per22 0 +per23 per23 0 +per24 per24 0 +per25 per25 0 +per26 per26 0 +per27 per27 0 +per28 per28 0 +per29 per29 0 +per30 per30 0 +per31 per31 0 +per32 per32 0 +per33 per33 0 +per34 per34 0 +per35 per35 0 +per36 per36 0 +per37 per37 0 +per38 per38 0 +per39 per39 0 +per40 per40 0 +per41 per41 0 +per42 per42 0 +per43 per43 0 +per44 per44 0 +per45 per45 0 +per46 per46 0 +per47 per47 0 +per48 per48 0 +per49 per49 0 +per50 per50 0 +per51 per51 0 +per52 per52 0 +per53 per53 0 +per54 per54 0 +per55 per55 0 +per56 per56 0 +per57 per57 0 +per58 per58 0 +per59 per59 0 +per60 per60 0 +per61 per61 0 +per62 per62 0 +per63 per63 0 +per64 per64 0 +per65 per65 0 +per66 per66 0 +per67 per67 0 +per68 per68 0 +per69 per69 0 +per70 per70 0 +per71 per71 0 +per72 per72 0 +per73 per73 0 +per74 per74 0 +per75 per75 0 +per76 per76 0 +per77 per77 0 +per78 per78 0 +per79 per79 0 +per80 per80 0 +per81 per81 0 +per82 per82 0 +per83 per83 0 +per84 per84 0 +per85 per85 0 +per86 per86 0 +per87 per87 0 +per88 per88 0 +per89 per89 0 +per90 per90 0 +per91 per91 0 +per92 per92 0 +per93 per93 0 +per94 per94 0 +per95 per95 0 +per96 per96 0 +per97 per97 0 +per98 per98 0 +per99 per99 0 +per100 per100 0 +per101 per101 0 +per102 per102 0 +per103 per103 0 +per104 per104 0 +per105 per105 0 +per106 per106 0 +per107 per107 0 +per108 per108 0 +per109 per109 0 +per110 per110 0 +per111 per111 0 +per112 per112 0 +per113 per113 0 +per114 per114 0 +per115 per115 0 +per116 per116 0 +per117 per117 0 +per118 per118 0 +per119 per119 0 +per120 per120 0 +per121 per121 0 +per122 per122 0 +per123 per123 0 +per124 per124 0 +per125 per125 0 +per126 per126 0 +per127 per127 0 +per128 per128 0 +per129 per129 0 +per130 per130 0 +per131 per131 0 +per132 per132 0 +per133 per133 0 +per134 per134 0 +per135 per135 0 +per136 per136 0 +per137 per137 0 +per138 per138 0 +per139 per139 0 +per140 per140 0 +per141 per141 0 +per142 per142 0 +per143 per143 0 +per144 per144 0 +per145 per145 0 +per146 per146 0 +per147 per147 0 +per148 per148 0 +per149 per149 0 +per150 per150 0 +per151 per151 0 +per152 per152 0 +per153 per153 0 +per154 per154 0 +per155 per155 0 +per156 per156 0 +per157 per157 0 +per158 per158 0 +per159 per159 0 +per160 per160 0 +per161 per161 0 +per162 per162 0 +per163 per163 0 +per164 per164 0 +per165 per165 0 +per166 per166 0 +per167 per167 0 +per168 per168 0 +per169 per169 0 +per170 per170 0 +per171 per171 0 +per172 per172 0 +per173 per173 0 +per174 per174 0 +per175 per175 0 +per176 per176 0 +per177 per177 0 +per178 per178 0 +per179 per179 0 +per180 per180 0 +per181 per181 0 +per182 per182 0 +per183 per183 0 +per184 per184 0 +per185 per185 0 +per186 per186 0 +per187 per187 0 +per188 per188 0 +per189 per189 0 +per190 per190 0 +per191 per191 0 +per192 per192 0 +per193 per193 0 +per194 per194 0 +per195 per195 0 +per196 per196 0 +per197 per197 0 +per198 per198 0 +per199 per199 0 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.cluster3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.cluster3 Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+per0 per0\t0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n+per1 per1\t1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n+per2 per2\t2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n+per3 per3\t3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 \n+per4 per4\t4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 1 1 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per195 per195 per198 per198 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.630000 0.7603 NA\n+ per195 per195 per199 per199 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.550000 0.7603 NA\n+ per196 per196 per197 per197 UN NA 0.0000 1.0000 0.0000 0.5000 -1 0.670000 0.7603 NA\n+ per196 per196 per198 per198 UN NA 0.5708 0.4292 0.0000 0.2146 -1 0.640000 0.7603 NA\n+ per196 per196 per199 per199 UN NA 0.7683 0.2317 0.0000 0.1158 0 0.640000 0.7603 NA\n+ per197 per197 per198 per198 UN NA 0.8877 0.1123 0.0000 0.0561 -1 0.610000 0.7603 NA\n+ per197 per197 per199 per199 UN NA 0.7989 0.1210 0.0801 0.1406 0 0.670000 0.7603 NA\n+ per198 per198 per199 per199 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.620000 0.7603 NA\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.log Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,13 @@ +PLINK v1.90p 64-bit (16 Jun 2020) +Options in effect: + --dummy 200 50 + +Hostname: p-body.local +Working directory: /Users/alexanderostrovsky/Desktop/testinggalaxy/galaxy/tools/myTools/plink/test-data +Start time: Fri Sep 11 14:29:52 2020 + +Random number seed: 1599859792 +32768 MB RAM detected; reserving 16384 MB for main workspace. +Dummy data (200 people, 50 SNPs) written to plink.bed + plink.bim + plink.fam . + +End time: Fri Sep 11 14:29:52 2020 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.mds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.mds Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,201 @@\n+ FID IID SOL C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 \n+ per0 per0 0 -0.11969 -0.00212532 0.0560104 -0.0190235 -0.040261 -0.00876349 -0.0930007 0.00271093 0.0204072 -0.000671749 \n+ per1 per1 0 -0.0278499 0.0105489 0.0414116 0.0213528 0.0202965 0.0114894 0.0272841 0.0433732 0.0205355 -0.0126483 \n+ per2 per2 0 -0.000595654 -0.0415623 0.0205774 0.0116205 -0.0508187 -0.047104 0.00888019 0.0300681 0.024778 -0.0133809 \n+ per3 per3 0 0.0894235 0.0400176 0.0386428 -0.0530706 0.0117964 -0.0629335 -0.00822075 -0.0154861 -0.0095255 0.0116565 \n+ per4 per4 0 -0.104859 0.0633037 0.055194 0.0306549 -0.0223837 0.110542 0.0214376 0.0201186 0.00480295 -0.0384674 \n+ per5 per5 0 -0.0493979 0.0776136 0.00801137 0.0151327 -0.0172491 0.0502627 0.0360993 -0.0901842 0.00151495 0.0214954 \n+ per6 per6 0 0.110491 0.0323241 0.00779048 0.0842718 -0.0150535 -0.0200886 -0.0833879 0.0369887 -0.03852 0.0396762 \n+ per7 per7 0 0.114085 0.067549 -0.0237815 0.0601414 0.0176698 -0.0528068 0.012001 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0.0912875 -0.0685226 0.0592062 0.0393948 \n+ per190 per190 0 0.0294151 0.0199075 0.0248547 0.0158896 -0.0567575 -0.0656703 -0.0351958 0.0328744 -0.0634074 -0.0536923 \n+ per191 per191 0 -0.0494908 -0.126648 -0.0207741 -0.0203337 0.00544623 -0.0995462 0.0120119 0.0289639 -0.0388084 0.107087 \n+ per192 per192 0 0.0587259 -0.0196195 -0.0784685 0.0334064 -0.00570562 -0.051163 0.0505859 0.0171299 -0.0408725 -0.0143214 \n+ per193 per193 0 0.00158027 -0.0195612 0.0223618 0.0722066 -0.0322288 0.0873251 0.00741496 -0.0892394 -0.118022 0.00097738 \n+ per194 per194 0 -0.0351567 0.0360887 0.043634 0.0779974 0.0169241 -0.0959623 -0.0640178 -0.0108878 0.0616811 0.0138587 \n+ per195 per195 0 0.0616434 0.0584186 0.137838 0.0453281 0.140026 0.0421443 0.0202498 0.0181262 0.0539752 0.0960736 \n+ per196 per196 0 0.0668722 -0.0318635 -0.0588643 -0.0298485 -0.0114425 0.0185845 0.0417334 0.0613701 0.0408116 -0.0550014 \n+ per197 per197 0 0.00778777 0.0288746 -0.0951566 0.0283417 -0.0641924 -0.00203804 0.0272766 -0.0309509 0.0469551 -0.0386219 \n+ per198 per198 0 0.0554029 -0.0581836 0.0660059 -0.0458483 -0.0261595 -0.0633392 0.0239955 -0.00033192 -0.0155617 0.034606 \n+ per199 per199 0 0.0499619 0.0382742 -0.142471 0.0776297 -0.0152763 -0.0855144 0.0173938 -0.0623128 -0.00544088 -0.0139453 \n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.mds.eigenval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.mds.eigenval Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +0.792632 +0.748354 +0.72666 +0.708723 +0.655709 +0.647763 +0.634687 +0.608235 +0.600101 +0.580645 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink.prune.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.prune.in Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,50 @@ +snp0 +snp1 +snp2 +snp3 +snp4 +snp5 +snp6 +snp7 +snp8 +snp9 +snp10 +snp11 +snp12 +snp13 +snp14 +snp15 +snp16 +snp17 +snp18 +snp19 +snp20 +snp21 +snp22 +snp23 +snp24 +snp25 +snp26 +snp27 +snp28 +snp29 +snp30 +snp31 +snp32 +snp33 +snp34 +snp35 +snp36 +snp37 +snp38 +snp39 +snp40 +snp41 +snp42 +snp43 +snp44 +snp45 +snp46 +snp47 +snp48 +snp49 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_2.bed |
| b |
| Binary file test-data/plink_2.bed has changed |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_2.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_2.bim Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,300 @@ +1 snp0 0 0 A B +1 snp1 0 1 B A +1 snp2 0 2 A B +1 snp3 0 3 B A +1 snp4 0 4 A B +1 snp5 0 5 A B +1 snp6 0 6 A B +1 snp7 0 7 B A +1 snp8 0 8 A B +1 snp9 0 9 B A +1 snp10 0 10 A B +1 snp11 0 11 A B +1 snp12 0 12 B A +1 snp13 0 13 B A +1 snp14 0 14 B A +1 snp15 0 15 A B +1 snp16 0 16 B A +1 snp17 0 17 B A +1 snp18 0 18 B A +1 snp19 0 19 B A +1 snp20 0 20 B A +1 snp21 0 21 B A +1 snp22 0 22 A B +1 snp23 0 23 A B +1 snp24 0 24 A B +1 snp25 0 25 B A +1 snp26 0 26 B A +1 snp27 0 27 B A +1 snp28 0 28 A B +1 snp29 0 29 A B +1 snp30 0 30 B A +1 snp31 0 31 B A +1 snp32 0 32 A B +1 snp33 0 33 A B +1 snp34 0 34 B A +1 snp35 0 35 B A +1 snp36 0 36 B A +1 snp37 0 37 B A +1 snp38 0 38 B A +1 snp39 0 39 A B +1 snp40 0 40 B A +1 snp41 0 41 A B +1 snp42 0 42 A B +1 snp43 0 43 B A +1 snp44 0 44 A B +1 snp45 0 45 A B +1 snp46 0 46 A B +1 snp47 0 47 A B +1 snp48 0 48 A B +1 snp49 0 49 B A +1 snp50 0 50 A B +1 snp51 0 51 B A +1 snp52 0 52 B A +1 snp53 0 53 B A +1 snp54 0 54 B A +1 snp55 0 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+1 snp210 0 210 B A +1 snp211 0 211 B A +1 snp212 0 212 B A +1 snp213 0 213 A B +1 snp214 0 214 B A +1 snp215 0 215 A B +1 snp216 0 216 B A +1 snp217 0 217 A B +1 snp218 0 218 B A +1 snp219 0 219 B A +1 snp220 0 220 B A +1 snp221 0 221 A B +1 snp222 0 222 B A +1 snp223 0 223 A B +1 snp224 0 224 A B +1 snp225 0 225 B A +1 snp226 0 226 A B +1 snp227 0 227 B A +1 snp228 0 228 B A +1 snp229 0 229 B A +1 snp230 0 230 A B +1 snp231 0 231 B A +1 snp232 0 232 B A +1 snp233 0 233 A B +1 snp234 0 234 B A +1 snp235 0 235 B A +1 snp236 0 236 B A +1 snp237 0 237 B A +1 snp238 0 238 B A +1 snp239 0 239 B A +1 snp240 0 240 A B +1 snp241 0 241 B A +1 snp242 0 242 B A +1 snp243 0 243 B A +1 snp244 0 244 B A +1 snp245 0 245 B A +1 snp246 0 246 A B +1 snp247 0 247 A B +1 snp248 0 248 A B +1 snp249 0 249 B A +1 snp250 0 250 B A +1 snp251 0 251 A B +1 snp252 0 252 B A +1 snp253 0 253 A B +1 snp254 0 254 B A +1 snp255 0 255 B A +1 snp256 0 256 B A +1 snp257 0 257 A B +1 snp258 0 258 A B +1 snp259 0 259 A B +1 snp260 0 260 B A +1 snp261 0 261 A B +1 snp262 0 262 A B +1 snp263 0 263 B A +1 snp264 0 264 A B +1 snp265 0 265 B A +1 snp266 0 266 B A +1 snp267 0 267 A B +1 snp268 0 268 A B +1 snp269 0 269 B A +1 snp270 0 270 A B +1 snp271 0 271 A B +1 snp272 0 272 B A +1 snp273 0 273 A B +1 snp274 0 274 B A +1 snp275 0 275 A B +1 snp276 0 276 A B +1 snp277 0 277 A B +1 snp278 0 278 B A +1 snp279 0 279 B A +1 snp280 0 280 B A +1 snp281 0 281 B A +1 snp282 0 282 A B +1 snp283 0 283 B A +1 snp284 0 284 A B +1 snp285 0 285 A B +1 snp286 0 286 B A +1 snp287 0 287 B A +1 snp288 0 288 A B +1 snp289 0 289 A B +1 snp290 0 290 A B +1 snp291 0 291 B A +1 snp292 0 292 A B +1 snp293 0 293 A B +1 snp294 0 294 A B +1 snp295 0 295 A B +1 snp296 0 296 A B +1 snp297 0 297 B A +1 snp298 0 298 B A +1 snp299 0 299 A B |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_2.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_2.fam Mon Sep 21 10:09:22 2020 +0000 |
| b |
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2\n+per484 per484 0 0 2 2\n+per485 per485 0 0 2 1\n+per486 per486 0 0 2 1\n+per487 per487 0 0 2 1\n+per488 per488 0 0 2 2\n+per489 per489 0 0 2 1\n+per490 per490 0 0 2 1\n+per491 per491 0 0 2 1\n+per492 per492 0 0 2 2\n+per493 per493 0 0 2 1\n+per494 per494 0 0 2 2\n+per495 per495 0 0 2 2\n+per496 per496 0 0 2 2\n+per497 per497 0 0 2 2\n+per498 per498 0 0 2 1\n+per499 per499 0 0 2 1\n' |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_2.log Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +PLINK v1.90p 64-bit (16 Jun 2020) +Options in effect: + --dummy 500 300 + +Hostname: p-body.local +Working directory: /Users/alexanderostrovsky/Desktop/testinggalaxy/galaxy/tools/myTools/plink/test-data +Start time: Mon Sep 14 15:29:09 2020 + +Random number seed: 1600122549 +32768 MB RAM detected; reserving 16384 MB for main workspace. +Dummy data (500 people, 300 SNPs) written to plink.bed + plink.bim + plink.fam +. + +End time: Mon Sep 14 15:29:09 2020 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_log.txt Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,29 @@ +PLINK v1.90p 64-bit (16 Jun 2020) +Options in effect: + --bfile plink_input/plink_input + --indep-pairwise 50 5 0.2 + --make-bed + --out plink_output/plink_output + +Hostname: p-body.local +Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmpzq_so7fd/job_working_directory/000/90/working +Start time: Tue Sep 15 12:47:24 2020 + +Random number seed: 1600199244 +32768 MB RAM detected; reserving 16384 MB for main workspace. +50 variants loaded from .bim file. +200 people (0 males, 200 females) loaded from .fam. +200 phenotype values loaded from .fam. +Using 1 thread (no multithreaded calculations invoked). +Before main variant filters, 200 founders and 0 nonfounders present. +Calculating allele frequencies... done. +50 variants and 200 people pass filters and QC. +Among remaining phenotypes, 101 are cases and 99 are controls. +--make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim + +plink_output/plink_output.fam ... done. +Pruned 0 variants from chromosome 1, leaving 50. +Pruning complete. 0 of 50 variants removed. +Marker lists written to plink_output/plink_output.prune.in and +plink_output/plink_output.prune.out . + +End time: Tue Sep 15 12:47:24 2020 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_output.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_output.log Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,42 @@ +PLINK v1.90p 64-bit (16 Jun 2020) +Options in effect: + --adjust gc log10 qq-plot + --assoc mperm=10000 fisher-midp + --bfile plink_input/plink_input + --logistic perm genedrop perm-count dominant hide-covar beta intercept + --make-bed + --out plink_output/plink_output + +Hostname: p-body.local +Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmp78g2r600/job_working_directory/000/94/working +Start time: Wed Sep 16 16:43:34 2020 + +Random number seed: 1600299814 +32768 MB RAM detected; reserving 16384 MB for main workspace. +50 variants loaded from .bim file. +200 people (0 males, 200 females) loaded from .fam. +200 phenotype values loaded from .fam. +Using up to 11 threads (change this with --threads). +Before main variant filters, 200 founders and 0 nonfounders present. +Calculating allele frequencies... done. +50 variants and 200 people pass filters and QC. +Among remaining phenotypes, 101 are cases and 99 are controls. +--make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim + +plink_output/plink_output.fam ... done. +Writing C/C --assoc report to plink_output/plink_output.assoc.fisher ... +done. +--adjust: Genomic inflation est. lambda (based on median chisq) = 1.22743. +--adjust values (50 variants) written to +plink_output/plink_output.assoc.fisher.adjusted . +10000 max(T) permutations complete. +Permutation test report written to plink_output/plink_output.assoc.fisher.mperm +. +Writing logistic model association results to +plink_output/plink_output.assoc.logistic ... done. +--adjust: Genomic inflation est. lambda (based on median chisq) = 1.16136. +--adjust values (50 variants) written to +plink_output/plink_output.assoc.logistic.adjusted . +579 (adaptive) permutations complete. +Permutation test report written to plink_output/plink_output.assoc.logistic.perm . + +End time: Wed Sep 16 16:43:34 2020 |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plink_test.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink_test.bim Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,50 @@ +1 snp0 0 0 A B +1 snp1 0 1 A B +1 snp2 0 2 A B +1 snp3 0 3 B A +1 snp4 0 4 B A +1 snp5 0 5 B A +1 snp6 0 6 A B +1 snp7 0 7 A B +1 snp8 0 8 B A +1 snp9 0 9 A B +1 snp10 0 10 B A +1 snp11 0 11 B A +1 snp12 0 12 B A +1 snp13 0 13 A B +1 snp14 0 14 B A +1 snp15 0 15 A B +1 snp16 0 16 A B +1 snp17 0 17 B A +1 snp18 0 18 B A +1 snp19 0 19 A B +1 snp20 0 20 A B +1 snp21 0 21 A B +1 snp22 0 22 A B +1 snp23 0 23 B A +1 snp24 0 24 A B +1 snp25 0 25 A B +1 snp26 0 26 B A +1 snp27 0 27 A B +1 snp28 0 28 B A +1 snp29 0 29 B A +1 snp30 0 30 A B +1 snp31 0 31 B A +1 snp32 0 32 B A +1 snp33 0 33 A B +1 snp34 0 34 B A +1 snp35 0 35 B A +1 snp36 0 36 A B +1 snp37 0 37 A B +1 snp38 0 38 B A +1 snp39 0 39 B A +1 snp40 0 40 B A +1 snp41 0 41 B A +1 snp42 0 42 B A +1 snp43 0 43 A B +1 snp44 0 44 A B +1 snp45 0 45 A B +1 snp46 0 46 A B +1 snp47 0 47 B A +1 snp48 0 48 B A +1 snp49 0 49 A B |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/plinke.genome --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plinke.genome Mon Sep 21 10:09:22 2020 +0000 |
| b |
| b'@@ -0,0 +1,19901 @@\n+ FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST PPC RATIO\n+ per0 per0 per1 per1 UN NA 0.7683 0.2317 0.0000 0.1158 0 0.640000 0.7603 NA\n+ per0 per0 per2 per2 UN NA 0.5511 0.4489 0.0000 0.2244 -1 0.630000 0.0786 0.0000\n+ per0 per0 per3 per3 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.580000 0.7603 NA\n+ per0 per0 per4 per4 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.620000 0.0786 0.0000\n+ per0 per0 per5 per5 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.600000 0.0786 0.0000\n+ per0 per0 per6 per6 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.550000 0.7603 NA\n+ per0 per0 per7 per7 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.570000 0.7603 NA\n+ per0 per0 per8 per8 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.500000 0.7603 NA\n+ per0 per0 per9 per9 UN NA 0.0000 1.0000 0.0000 0.5000 -1 0.560000 0.7603 NA\n+ per0 per0 per10 per10 UN NA 0.7989 0.2010 0.0001 0.1006 -1 0.650000 0.0786 0.0000\n+ per0 per0 per11 per11 UN NA 0.9587 0.0413 0.0000 0.0207 0 0.630000 0.7603 NA\n+ per0 per0 per12 per12 UN NA 0.8877 0.1123 0.0000 0.0561 -1 0.610000 0.0786 0.0000\n+ per0 per0 per13 per13 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.590000 0.0786 0.0000\n+ per0 per0 per14 per14 UN NA 0.7399 0.2601 0.0000 0.1301 0 0.630000 0.7603 NA\n+ per0 per0 per15 per15 UN NA 0.6054 0.3946 0.0000 0.1973 -1 0.570000 0.0786 0.0000\n+ per0 per0 per16 per16 UN NA 0.4440 0.5560 0.0000 0.2780 0 0.670000 0.7603 NA\n+ per0 per0 per17 per17 UN NA 0.8888 0.0000 0.1112 0.1112 0 0.660000 0.7603 NA\n+ per0 per0 per18 per18 UN NA 0.5708 0.4292 0.0000 0.2146 -1 0.640000 0.7603 NA\n+ per0 per0 per19 per19 UN NA 0.7683 0.2317 0.0000 0.1158 0 0.640000 0.7603 NA\n+ per0 per0 per20 per20 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.570000 0.0786 0.0000\n+ per0 per0 per21 per21 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.620000 0.7603 NA\n+ per0 per0 per22 per22 UN NA 0.6391 0.3606 0.0002 0.1806 0 0.670000 0.7603 NA\n+ per0 per0 per23 per23 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.630000 0.0786 0.0000\n+ per0 per0 per24 per24 UN NA 0.4611 0.5389 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| diff -r 000000000000 -r a98caf1d69ab test-data/stats.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.log Mon Sep 21 10:09:22 2020 +0000 |
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| @@ -0,0 +1,40 @@ +PLINK v1.90p 64-bit (16 Jun 2020) +Options in effect: + --bfile plink_input/plink_input + --check-sex ycount 0.2 0.8 10 200 + --freq + --hardy + --het + --make-bed + --missing + --out plink_output/plink_output + +Hostname: p-body.local +Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmpzq_so7fd/job_working_directory/000/89/working +Start time: Tue Sep 15 10:53:23 2020 + +Random number seed: 1600192403 +32768 MB RAM detected; reserving 16384 MB for main workspace. +50 variants loaded from .bim file. +200 people (0 males, 200 females) loaded from .fam. +200 phenotype values loaded from .fam. +Using 1 thread (no multithreaded calculations invoked). +Before main variant filters, 200 founders and 0 nonfounders present. +Calculating allele frequencies... done. +--freq: Allele frequencies (founders only) written to +plink_output/plink_output.frq . +--missing: Sample missing data report written to +plink_output/plink_output.imiss, and variant-based missing data report written +to plink_output/plink_output.lmiss. +--hardy: Writing Hardy-Weinberg report (founders only) to +plink_output/plink_output.hwe ... done. +50 variants and 200 people pass filters and QC. +Among remaining phenotypes, 101 are cases and 99 are controls. +Warning: No Y chromosome data for --check-sex ycount. +--check-sex: 26 Xchr and 0 Ychr variant(s) scanned, 31 problems detected. +Report written to plink_output/plink_output.sexcheck . +--make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim + +plink_output/plink_output.fam ... done. +--het: 24 variants scanned, report written to plink_output/plink_output.het . + +End time: Tue Sep 15 10:53:23 2020 |
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| @@ -0,0 +1,34 @@ +##fileformat=VCFv4.1 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT wgs2 +chr1 500 . C T . . DP=10 GT 1/1 +chr1 1000 . A G . . DP=10 GT 0/1 +chr1 1500 . G A . . DP=10 GT 1/0 +chr1 2000 . G A . . DP=10 GT 1/1 +chr1 2500 . A G . . DP=10 GT 0/1 +chr1 3000 . G C . . DP=10 GT 1/0 +chr1 3500 . G T . . DP=10 GT 1/1 +chr1 4000 . A G . . DP=10 GT 0/1 +chr1 4500 . A C . . DP=10 GT 1/0 +chr1 5000 . A G . . DP=10 GT 1/1 +chr1 5500 . C T . . DP=10 GT 0/1 +chr1 6000 . C A . . DP=10 GT 1/0 +chr1 6500 . C T . . DP=10 GT 1/1 +chr1 7000 . G T . . DP=10 GT 0/1 +chr1 7500 . G C . . DP=10 GT 1/0 +chr1 8000 . T G . . DP=10 GT 1/1 +chr1 8500 . T A . . DP=10 GT 0/1 +chr1 9000 . C T . . DP=10 GT 1/0 +chr1 9500 . G A . . DP=10 GT 1/1 +chr1 10000 . A G . . DP=10 GT 0/1 +chr1 10500 . T C . . DP=10 GT 1/0 +chr1 11000 . A G . . DP=10 GT 1/1 +chr1 11500 . C T . . DP=10 GT 0/1 +chr1 12000 . A G . . DP=10 GT 1/0 +chr1 12500 . C G . . DP=10 GT 1/1 +chr1 13000 . T C . . DP=10 GT 0/1 +chr1 13500 . G T . . DP=10 GT 1/0 +chr1 14000 . A C . . DP=10 GT 1/1 +chr1 14500 . A G . . DP=10 GT 0/1 +chr1 15000 . T G . . DP=10 GT 1/0 |
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| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/test2_out.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_out.fam Mon Sep 21 10:09:22 2020 +0000 |
| b |
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| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/test5_out.bed |
| b |
| Binary file test-data/test5_out.bed has changed |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/test5_out.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5_out.bim Mon Sep 21 10:09:22 2020 +0000 |
| b |
| @@ -0,0 +1,50 @@ +1 snp0 0 0 A B +1 snp1 0 1 A B +1 snp2 0 2 A B +1 snp3 0 3 B A +1 snp4 0 4 B A +1 snp5 0 5 B A +1 snp6 0 6 A B +1 snp7 0 7 A B +1 snp8 0 8 B A +1 snp9 0 9 A B +1 snp10 0 10 B A +1 snp11 0 11 B A +1 snp12 0 12 B A +1 snp13 0 13 A B +1 snp14 0 14 B A +1 snp15 0 15 A B +1 snp16 0 16 A B +1 snp17 0 17 B A +1 snp18 0 18 B A +1 snp19 0 19 A B +1 snp20 0 20 A B +1 snp21 0 21 A B +1 snp22 0 22 A B +1 snp23 0 23 B A +1 snp24 0 24 A B +1 snp25 0 25 A B +1 snp26 0 26 B A +1 snp27 0 27 A B +1 snp28 0 28 B A +1 snp29 0 29 B A +1 snp30 0 30 A B +1 snp31 0 31 B A +1 snp32 0 32 B A +1 snp33 0 33 A B +1 snp34 0 34 B A +1 snp35 0 35 B A +1 snp36 0 36 A B +1 snp37 0 37 A B +1 snp38 0 38 B A +1 snp39 0 39 B A +1 snp40 0 40 B A +1 snp41 0 41 B A +1 snp42 0 42 B A +1 snp43 0 43 A B +1 snp44 0 44 A B +1 snp45 0 45 A B +1 snp46 0 46 A B +1 snp47 0 47 B A +1 snp48 0 48 B A +1 snp49 0 49 A B |
| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/test5_out.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5_out.fam Mon Sep 21 10:09:22 2020 +0000 |
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| diff -r 000000000000 -r a98caf1d69ab test-data/test6_out.bed |
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| diff -r 000000000000 -r a98caf1d69ab test-data/testing.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testing.txt Mon Sep 21 10:09:22 2020 +0000 |
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| diff -r 000000000000 -r a98caf1d69ab test-data/update_cols.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/update_cols.txt Mon Sep 21 10:09:22 2020 +0000 |
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| b |
| diff -r 000000000000 -r a98caf1d69ab test-data/vcf_out.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_out.fam Mon Sep 21 10:09:22 2020 +0000 |
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