| Previous changeset 8:16d22eee0fe3 (2021-12-02) Next changeset 10:2c0ac05fe240 (2023-11-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401" |
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modified:
plink.xml test-data/out.assoc.logistic.perm test-data/out.ped test-data/plink.cluster1 test-data/plink.cluster3 test-data/plink.genome test-data/test2_out.bed test-data/test2_out.bim test-data/test2_out.fam |
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removed:
test-data/plink.log 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.log |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd plink.xml --- a/plink.xml Thu Dec 02 16:20:30 2021 +0000 +++ b/plink.xml Sun Dec 19 15:53:35 2021 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\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@\'>3</token>\n+ <token name=\'@TOOL_VERSION@\'>1.90b6.21</token>\n+ <token name=\'@VERSION_SUFFIX@\'>0</token>\n <xml name=\'template_sanitizer\'>\n <sanitizer>\n <valid initial=\'default\'>\n@@ -37,12 +37,19 @@\n </valid>\n </sanitizer>\n </xml>\n+ <xml name="log_out_assert">\n+ <output name="plink_log">\n+ <assert_contents>\n+ <has_text text="End time:"/>\n+ </assert_contents>\n+ </output>\n+ </xml>\n </macros>\n <xrefs>\n <xref type="bio.tools">plink</xref>\n </xrefs>\n <requirements>\n- <requirement type=\'package\' version=\'1.90b6.18\'>plink</requirement>\n+ <requirement type=\'package\' version=\'@TOOL_VERSION@\'>plink</requirement>\n </requirements>\n <command detect_errors=\'exit_code\'><![CDATA[\n \n@@ -55,17 +62,17 @@\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+ && ln -s \'$functions.bmerge.bed.extra_files_path\'/RgeneticsData.bed bmerge_files/bmerge_input.bed\n+ && ln -s \'$functions.bmerge.bed.extra_files_path\'/RgeneticsData.bim bmerge_files/bmerge_input.bim\n+ && ln -s \'$functions.bmerge.bed.extra_files_path\'/RgeneticsData.fam bmerge_files/bmerge_input.fam\n #end if\n #end if\n \n \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+ && ln -s \'$inputs.inputs.bed.extra_files_path\'/RgeneticsData.bed plink_input/plink_input.bed\n+ && ln -s \'$inputs.inputs.bed.extra_files_path\'/RgeneticsData.bim plink_input/plink_input.bim\n+ && ln -s \'$inputs.inputs.bed.extra_files_path\'/RgeneticsData.fam plink_input/plink_input.fam\n && plink --bfile plink_input/plink_input\n #elif $inputs.inputs.filetype == \'vcf\':\n #if $inputs.inputs.input.is_of_type(\'bcf\'):\n@@ -402,6 +409,10 @@\n && find ./assoc_out/. -type f -exec mv {} {}.txt \';\'\n #end if\n #end if\n+ && mkdir \'$plink_out.extra_files_path\'\n+ && cp plink_output/plink_output.bed \'$plink_out.extra_files_path\'/RgeneticsData.bed\n+ && cp plink_output/plink_output.bim \'$plink_out.extra_files_path\'/RgeneticsData.bim\n+ && cp plink_output/plink_output.fam \'$plink_out.extra_files_path\'/RgeneticsData.fam\n ]]></command>\n <inputs>\n <section name=\'inputs\' title=\'Data inputs\' expanded=\'true\'>\n@@ -412,8 +423,6 @@\n </param>\n <when value=\'bfile\'>\n <param format=\'pbed\' name=\'bed\' type=\'data\' label=\'plink bed file\'/>\n- <param format=\'tabular,tsv\' name=\'bim\' type=\'data\' label=\'plink bim file\'/>\n- <param format=\'txt\' name=\'fam\' type=\'data\' label=\'plink fam file\'/>\n </when>\n <when value=\'vcf\'>\n <param name=\'input\' format=\'vcf,vcf_bgzip,bcf\' type=\'data\' label=\'VCF/BCF Input file\'/>\n@@ -671,9 +680,7 @@\n </param>\n <when value=\'No\'/>\n <when value=\'Yes\'>\n- <param format=\'binary\' name=\'bed\' type=\'data\' label=\'plink bed file\'/>\n- <param format=\'tabular,tsv\' name=\'bim\' type=\'data\' label=\'plink bim file\'/>\n- <param format=\'tabular,tsv\' name=\'fam\' type=\'data\' label'..b'out.bed\' compare=\'sim_size\'/>\n- <element name=\'plink_bim\' file=\'test6_out.bim\'/>\n- <element name=\'plink_fam\' file=\'test6_out.fam\'/>\n- </output_collection>\n+ <output name="plink_out">\n+ <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare=\'sim_size\'/>\n+ <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/>\n+ <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/>\n+ </output>\n+ <expand macro="log_out_assert"/>\n <output name=\'mds\' value=\'plink.mds\' compare=\'sim_size\'/>\n <output name=\'cluster1\' value=\'plink.cluster1\' compare=\'sim_size\'/>\n <output name=\'cluster2\' value=\'plink.cluster2\' compare=\'sim_size\'/>\n@@ -1291,13 +1311,15 @@\n <output name=\'eigenvals\' value=\'plink.mds.eigenval\' compare=\'sim_size\'/>\n </test>\n \n- <test expect_num_outputs=\'8\'>\n+ <test expect_num_outputs=\'5\'>\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+ <param name=\'bed\' value=\'\' ftype="pbed">\n+ <composite_data value="plink.bim"/>\n+ <composite_data value="plink.bed"/>\n+ <composite_data value="plink.fam"/>\n+ </param>\n </conditional>\n </section>\n <conditional name=\'functions\'>\n@@ -1328,11 +1350,12 @@\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="plink_out">\n+ <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare=\'sim_size\'/>\n+ <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/>\n+ <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/>\n+ </output>\n+ <expand macro="log_out_assert"/>\n <output_collection name=\'assoc_outfiles\' type=\'list\' count=\'2\'>\n <element name=\'plink_output.assoc.fisher.mperm\' value=\'out.assoc.fisher.mperm\' compare=\'sim_size\'/>\n <element name=\'plink_output.assoc.fisher\' value=\'out.assoc.fisher\'/>\n@@ -1347,13 +1370,15 @@\n </output_collection>\n </test>\n \n- <test expect_num_outputs=\'6\'>\n+ <test expect_num_outputs=\'3\'>\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+ <param name=\'bed\' value=\'\' ftype="pbed">\n+ <composite_data value="plink.bim"/>\n+ <composite_data value="plink.bed"/>\n+ <composite_data value="plink.fam"/>\n+ </param>\n </conditional>\n </section>\n <conditional name=\'functions\'>\n@@ -1365,6 +1390,7 @@\n <param name=\'modifiers\' value=\'full,unbounded,nudge\'/>\n </conditional>\n </conditional>\n+ <expand macro="log_out_assert"/>\n <output name=\'genome\' file=\'out.genome\'/>\n </test>\n </tests>\n' |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/out.assoc.logistic.perm --- a/test-data/out.assoc.logistic.perm Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/out.assoc.logistic.perm Sun Dec 19 15:53:35 2021 +0000 |
| b |
| @@ -1,51 +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 snp0 11 22 + 1 snp1 18 88 + 1 snp2 8 13 + 1 snp3 17 71 + 1 snp4 5 6 + 1 snp5 13 33 + 1 snp6 5 6 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 snp8 12 28 + 1 snp9 5 6 + 1 snp10 8 13 + 1 snp11 6 6 + 1 snp12 15 43 + 1 snp13 21 707 + 1 snp14 9 16 + 1 snp15 17 78 + 1 snp16 5 6 + 1 snp17 20 172 + 1 snp18 12 27 + 1 snp19 8 13 + 1 snp20 20 198 + 1 snp21 17 77 + 1 snp22 19.5 176 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 snp24 5.5 6 + 1 snp25 10 18 + 1 snp26 14 36 + 1 snp27 8 12 + 1 snp28 8 13 + 1 snp29 5 6 + 1 snp30 8 12 + 1 snp31 16 61 + 1 snp32 16 58 + 1 snp33 19 135 + 1 snp34 6 6 + 1 snp35 9 16 + 1 snp36 20 171 + 1 snp37 9 15 + 1 snp38 16 58 + 1 snp39 8 13 + 1 snp40 14 37 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 snp42 14 39 + 1 snp43 12 28 + 1 snp44 18 113 + 1 snp45 20.5 376 + 1 snp46 12 28 + 1 snp47 6 6 + 1 snp48 18 112 1 snp49 6 6 |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/out.ped --- a/test-data/out.ped Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/out.ped Sun Dec 19 15:53:35 2021 +0000 |
| b |
| b'@@ -1,500 +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'..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 B A A B B B A A B A B A B B A A A A B B B A A A B B A B B B A A B A 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 A B B A A B A B A B B A A A B A 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 B A B A A A B A A B B B B A A B B B A B A B 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 A B A A A B B B B B A A A B B A 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 A B 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 16d22eee0fe3 -r 272aca44b3dd test-data/plink.cluster1 --- a/test-data/plink.cluster1 Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/plink.cluster1 Sun Dec 19 15:53:35 2021 +0000 |
| b |
| @@ -1,1 +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) 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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) +SOL-0 per0_per0(1) per82_per82(1) per133_per133(2) per48_per48(1) per94_per94(2) per114_per114(2) per153_per153(2) per23_per23(2) per51_per51(1) per128_per128(2) per98_per98(2) per102_per102(1) per1_per1(2) per179_per179(1) per143_per143(1) per56_per56(2) per73_per73(1) per193_per193(2) per127_per127(1) per38_per38(2) per141_per141(1) per132_per132(2) per52_per52(2) per129_per129(2) per184_per184(1) per3_per3(1) per164_per164(2) per198_per198(1) per9_per9(1) per175_per175(2) per5_per5(1) per76_per76(2) per30_per30(2) per163_per163(1) per147_per147(2) per19_per19(2) per196_per196(1) per124_per124(1) per130_per130(2) per54_per54(2) per121_per121(1) per151_per151(2) per78_per78(1) per16_per16(2) per40_per40(1) per144_per144(2) per65_per65(2) per92_per92(2) per190_per190(1) per185_per185(1) per93_per93(1) per22_per22(2) per135_per135(1) per161_per161(1) per103_per103(1) per41_per41(1) per59_per59(1) per106_per106(2) per63_per63(1) per71_per71(2) per191_per191(1) per6_per6(2) per35_per35(1) per33_per33(1) per108_per108(2) per44_per44(2) per138_per138(1) per104_per104(1) per120_per120(2) per113_per113(1) per86_per86(1) per69_per69(1) per74_per74(2) per119_per119(2) per142_per142(1) per72_per72(2) per2_per2(1) per27_per27(2) per64_per64(1) per17_per17(2) per169_per169(1) per21_per21(2) per177_per177(2) per99_per99(2) per25_per25(1) per43_per43(2) per123_per123(1) per85_per85(2) per18_per18(1) per28_per28(2) per50_per50(2) per100_per100(2) per105_per105(2) per118_per118(2) per150_per150(1) per46_per46(2) per83_per83(1) per95_per95(2) per58_per58(2) per8_per8(1) per13_per13(2) per125_per125(1) per154_per154(2) per155_per155(1) per89_per89(2) per10_per10(1) per156_per156(1) per194_per194(2) per111_per111(1) per158_per158(2) per42_per42(2) per70_per70(2) per84_per84(1) per137_per137(1) per45_per45(2) per79_per79(2) per157_per157(1) per11_per11(2) per24_per24(1) per116_per116(1) per61_per61(2) per136_per136(1) per12_per12(1) 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) per29_per29(2) per192_per192(1) per183_per183(1) per165_per165(2) per160_per160(2) per166_per166(1) per162_per162(2) per181_per181(1) per182_per182(1) per97_per97(1) per189_per189(2) per7_per7(2) per172_per172(1) per32_per32(2) per53_per53(1) per176_per176(2) per34_per34(1) per60_per60(2) per188_per188(1) per107_per107(2) per55_per55(1) per66_per66(2) per109_per109(1) per62_per62(2) per159_per159(1) per87_per87(2) per139_per139(1) per122_per122(2) per4_per4(1) per131_per131(2) per26_per26(2) per67_per67(1) per91_per91(1) per112_per112(2) per39_per39(1) per149_per149(2) per49_per49(1) per47_per47(2) per197_per197(1) per101_per101(2) per152_per152(1) per80_per80(1) per199_per199(2) per20_per20(2) per173_per173(1) per110_per110(1) per145_per145(2) per187_per187(1) per31_per31(2) per178_per178(1) per37_per37(2) per180_per180(1) per75_per75(1) per77_per77(2) per174_per174(1) per90_per90(2) per195_per195(1) per167_per167(1) per186_per186(2) per57_per57(2) per88_per88(1) per170_per170(2) per140_per140(1) per126_per126(2) |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/plink.cluster3 --- a/test-data/plink.cluster3 Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/plink.cluster3 Sun Dec 19 15:53:35 2021 +0000 |
| b |
| b'@@ -1,201 +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 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-per5 per5\t5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 3 3 3 2 2 1 1 1 1 1 1 1 1 0 0 0 0 0 \n-per6 per6\t6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n-per7 per7\t7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 5 5 5 5 5 4 4 4 2 2 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 \n-per8 per8\t8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 6 6 6 6 6 5 5 5 4 4 4 3 3 2 2 2 2 2 2 2 0 0 0 0 0 0 \n-per9 per9\t9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 '..b'6 46 45 45 45 45 45 45 45 45 45 45 45 45 45 45 44 44 44 44 43 43 43 43 43 43 43 43 43 43 43 43 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 \n+per194 per194\t194 193 192 191 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176 175 174 173 173 172 171 170 169 168 167 166 165 164 164 163 162 161 160 159 158 157 156 155 154 153 152 152 151 150 149 148 147 146 145 144 143 142 141 140 139 138 137 136 135 134 133 132 131 130 129 128 127 126 125 124 123 122 121 120 119 118 117 116 115 114 98 97 96 95 94 94 94 93 92 92 92 92 92 91 90 90 89 88 88 87 86 85 84 84 83 82 81 80 79 78 77 77 76 75 74 73 73 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 8 8 8 8 8 8 8 8 8 8 7 7 7 7 7 7 7 7 7 7 7 6 5 5 5 5 5 5 5 5 5 5 5 4 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n+per195 per195\t195 194 193 192 192 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176 175 174 174 173 172 171 170 169 168 167 166 165 84 83 83 83 83 82 82 82 82 82 82 82 82 82 81 80 80 79 78 78 78 78 77 76 75 74 73 72 72 72 72 72 72 72 72 72 72 71 71 71 71 70 70 70 70 70 70 70 70 70 70 70 70 70 70 69 69 69 69 68 68 68 68 68 68 68 68 68 68 67 67 66 65 64 63 63 62 61 61 61 61 60 59 59 58 57 56 56 56 56 55 55 54 54 53 52 51 51 50 49 49 49 49 49 48 47 47 46 45 44 44 43 42 42 41 41 40 39 38 37 37 37 36 35 34 33 32 31 30 30 29 28 28 27 27 27 26 25 24 23 22 22 21 20 19 18 17 16 16 15 14 13 12 11 10 9 8 7 6 3 3 2 1 0 0 0 0 \n+per196 per196\t196 195 194 193 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 17 17 17 17 17 16 16 16 16 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 3 3 3 3 3 3 3 3 3 3 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 \n+per197 per197\t197 196 195 194 193 192 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176 175 175 174 173 172 171 170 169 168 167 166 165 164 163 162 161 160 159 158 157 156 155 154 153 44 43 42 42 42 42 42 42 42 41 40 40 40 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 35 35 34 34 33 33 33 33 33 33 33 33 32 32 31 31 30 30 30 30 30 30 30 30 30 30 30 30 30 30 29 29 29 29 28 27 27 26 26 26 26 26 25 25 24 23 23 23 22 22 22 21 21 21 20 19 18 17 17 17 16 15 15 14 14 13 13 13 12 11 10 9 8 7 6 5 4 4 1 0 0 0 0 0 0 \n+per198 per198\t198 197 196 195 194 193 192 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176 149 148 147 146 145 144 143 143 143 143 143 142 141 140 139 138 137 137 137 137 136 136 136 136 135 134 133 132 131 130 129 128 127 126 125 124 123 122 121 120 119 118 117 116 116 116 115 114 113 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 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 \n+per199 per199\t199 198 197 196 195 194 193 192 191 190 189 188 187 186 185 184 183 182 181 180 179 178 177 176 175 174 173 172 171 170 169 168 167 166 165 164 163 162 161 160 159 158 157 156 155 154 153 152 151 150 149 148 147 146 145 144 143 142 141 140 139 138 137 136 135 134 133 132 131 130 129 128 127 126 125 124 123 122 121 120 119 118 117 116 115 114 113 112 111 110 109 108 107 106 105 104 103 102 101 100 99 98 97 96 95 94 93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 77 76 75 74 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54 53 52 39 38 37 36 35 35 35 34 33 32 31 30 29 28 28 27 27 27 26 26 26 25 24 23 22 21 21 20 19 15 14 14 13 13 13 12 11 10 9 8 7 6 5 4 4 1 0 0 0 0 0 0 \n \n' |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/plink.genome --- a/test-data/plink.genome Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/plink.genome Sun Dec 19 15:53:35 2021 +0000 |
| b |
| b'@@ -1,19901 +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 0.0000 0.2695 -1 0.680000 0.0786 0.0000\n- per0 per0 per25 per25 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.620000 0.0786 0.0000\n- per0 per0 per26 per26 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.570000 0.0786 0.0000\n- per0 per0 per27 per27 UN NA 0.7134 0.2866 0.0000 0.1433 0 0.620000 0.0786 0.0000\n- per0 per0 per28 per28 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.580000 0.7603 NA\n- per0 per0 per29 per29 UN NA 0.4440 0.5560 0.0000 0.2780 0 0.670000 0.7603 NA\n- per0 per0 per30 per30 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.640000 0.0786 0.0000\n- per0 per0 per31 per31 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.610000 0.7603 NA\n- per0 per0 per32 per32 UN NA 0.7989 0.0411 0.1600 0.1806 0 0.690000 0.0786 0.0000\n- per0 per0 per33 per33 UN NA 0.8888 0.0000 0.1112 0.1112 -1 0.660000 0.7603 NA\n- per0 per0 per34 per34 UN NA 0.8561 0.1439 0.0000 0.0720 -1 0.600000 0.7603 NA\n- per0 per0 per35 per35 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.560000 0.0786 0.0000\n- per0 per0 per36 per36 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.630000 0.7603 NA\n- per0 per0 per37 per37 UN NA 0.6054 0.3946 0.0000 0.1973 0 0.570000 0.7603 NA\n- per0 per0 per38 per38 UN NA 0.9219 0.0781 0.0000 0.0391 0 0.620000 0.7603 NA\n- per0 per0 per39 per39 UN '..b'198\tper198\tUN\tNA\t0.5708\t0.4292\t0.0000\t0.2146\t0\t0.640000\t0.7603\tNA\n+per189\tper189\tper199\tper199\tUN\tNA\t0.8561\t0.1439\t0.0000\t0.0720\t1\t0.600000\t0.0786\t0.0000\n+per190\tper190\tper191\tper191\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.630000\t0.0786\t0.0000\n+per190\tper190\tper192\tper192\tUN\tNA\t0.7989\t0.0011\t0.2000\t0.2005\t-1\t0.700000\t0.7603\tNA\n+per190\tper190\tper193\tper193\tUN\tNA\t0.4793\t0.5203\t0.0004\t0.2605\t0\t0.690000\t0.7603\tNA\n+per190\tper190\tper194\tper194\tUN\tNA\t0.5511\t0.4489\t0.0000\t0.2244\t0\t0.630000\t0.7603\tNA\n+per190\tper190\tper195\tper195\tUN\tNA\t0.4995\t0.5005\t0.0000\t0.2503\t-1\t0.600000\t0.7603\tNA\n+per190\tper190\tper196\tper196\tUN\tNA\t0.8570\t0.0000\t0.1430\t0.1430\t-1\t0.670000\t0.7603\tNA\n+per190\tper190\tper197\tper197\tUN\tNA\t0.7134\t0.2866\t0.0000\t0.1433\t-1\t0.620000\t0.0786\t0.0000\n+per190\tper190\tper198\tper198\tUN\tNA\t0.4440\t0.5560\t0.0000\t0.2780\t-1\t0.670000\t0.7603\tNA\n+per190\tper190\tper199\tper199\tUN\tNA\t0.8570\t0.0000\t0.1430\t0.1430\t0\t0.670000\t0.7603\tNA\n+per191\tper191\tper192\tper192\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.610000\t0.0786\t0.0000\n+per191\tper191\tper193\tper193\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.580000\t0.0786\t0.0000\n+per191\tper191\tper194\tper194\tUN\tNA\t0.4282\t0.5718\t0.0000\t0.2859\t0\t0.660000\t0.0786\t0.0000\n+per191\tper191\tper195\tper195\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.550000\t0.0786\t0.0000\n+per191\tper191\tper196\tper196\tUN\tNA\t0.6659\t0.3341\t0.0000\t0.1670\t-1\t0.600000\t0.0786\t0.0000\n+per191\tper191\tper197\tper197\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.590000\t0.0786\t0.0000\n+per191\tper191\tper198\tper198\tUN\tNA\t0.4282\t0.5718\t0.0000\t0.2859\t-1\t0.660000\t0.0786\t0.0000\n+per191\tper191\tper199\tper199\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.600000\t0.0786\t0.0000\n+per192\tper192\tper193\tper193\tUN\tNA\t0.7989\t0.1210\t0.0801\t0.1406\t0\t0.670000\t0.7603\tNA\n+per192\tper192\tper194\tper194\tUN\tNA\t0.6054\t0.3946\t0.0000\t0.1973\t0\t0.570000\t0.7603\tNA\n+per192\tper192\tper195\tper195\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.540000\t0.7603\tNA\n+per192\tper192\tper196\tper196\tUN\tNA\t0.6391\t0.2807\t0.0802\t0.2205\t-1\t0.690000\t0.7603\tNA\n+per192\tper192\tper197\tper197\tUN\tNA\t0.3196\t0.6400\t0.0404\t0.3604\t-1\t0.720000\t0.7603\tNA\n+per192\tper192\tper198\tper198\tUN\tNA\t0.7399\t0.2601\t0.0000\t0.1301\t-1\t0.630000\t0.7603\tNA\n+per192\tper192\tper199\tper199\tUN\tNA\t0.2960\t0.7040\t0.0000\t0.3520\t0\t0.690000\t0.7603\tNA\n+per193\tper193\tper194\tper194\tUN\tNA\t0.9219\t0.0781\t0.0000\t0.0391\t1\t0.620000\t0.7603\tNA\n+per193\tper193\tper195\tper195\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.630000\t0.7603\tNA\n+per193\tper193\tper196\tper196\tUN\tNA\t0.3996\t0.6004\t0.0000\t0.3002\t0\t0.640000\t0.7603\tNA\n+per193\tper193\tper197\tper197\tUN\tNA\t0.5511\t0.4489\t0.0000\t0.2244\t0\t0.630000\t0.7603\tNA\n+per193\tper193\tper198\tper198\tUN\tNA\t0.4611\t0.5389\t0.0000\t0.2695\t0\t0.680000\t0.7603\tNA\n+per193\tper193\tper199\tper199\tUN\tNA\t0.9219\t0.0781\t0.0000\t0.0391\t1\t0.620000\t0.7603\tNA\n+per194\tper194\tper195\tper195\tUN\tNA\t0.9587\t0.0413\t0.0000\t0.0207\t0\t0.630000\t0.7603\tNA\n+per194\tper194\tper196\tper196\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.580000\t0.7603\tNA\n+per194\tper194\tper197\tper197\tUN\tNA\t0.7399\t0.2601\t0.0000\t0.1301\t0\t0.630000\t0.7603\tNA\n+per194\tper194\tper198\tper198\tUN\tNA\t0.9587\t0.0013\t0.0400\t0.0407\t0\t0.640000\t0.7603\tNA\n+per194\tper194\tper199\tper199\tUN\tNA\t0.7683\t0.2317\t0.0000\t0.1158\t1\t0.640000\t0.7603\tNA\n+per195\tper195\tper196\tper196\tUN\tNA\t0.5919\t0.4081\t0.0000\t0.2040\t-1\t0.650000\t0.7603\tNA\n+per195\tper195\tper197\tper197\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.580000\t0.0786\t0.0000\n+per195\tper195\tper198\tper198\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t-1\t0.630000\t0.7603\tNA\n+per195\tper195\tper199\tper199\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.550000\t0.7603\tNA\n+per196\tper196\tper197\tper197\tUN\tNA\t0.0000\t1.0000\t0.0000\t0.5000\t-1\t0.670000\t0.7603\tNA\n+per196\tper196\tper198\tper198\tUN\tNA\t0.5708\t0.4292\t0.0000\t0.2146\t-1\t0.640000\t0.7603\tNA\n+per196\tper196\tper199\tper199\tUN\tNA\t0.7683\t0.2317\t0.0000\t0.1158\t0\t0.640000\t0.7603\tNA\n+per197\tper197\tper198\tper198\tUN\tNA\t0.8877\t0.1123\t0.0000\t0.0561\t-1\t0.610000\t0.7603\tNA\n+per197\tper197\tper199\tper199\tUN\tNA\t0.7989\t0.1210\t0.0801\t0.1406\t0\t0.670000\t0.7603\tNA\n+per198\tper198\tper199\tper199\tUN\tNA\t1.0000\t0.0000\t0.0000\t0.0000\t0\t0.620000\t0.7603\tNA\n' |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/plink.log --- a/test-data/plink.log Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -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 16d22eee0fe3 -r 272aca44b3dd test-data/plink_2.log --- a/test-data/plink_2.log Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -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 16d22eee0fe3 -r 272aca44b3dd test-data/plink_log.txt --- a/test-data/plink_log.txt Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -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 16d22eee0fe3 -r 272aca44b3dd test-data/plink_output.log --- a/test-data/plink_output.log Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,42 +0,0 @@ -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 16d22eee0fe3 -r 272aca44b3dd test-data/plink_test.bim --- a/test-data/plink_test.bim Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,50 +0,0 @@ -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 16d22eee0fe3 -r 272aca44b3dd test-data/plinke.genome --- a/test-data/plinke.genome Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,19901 +0,0 @@\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 0.0000 0.2695 -1 0.680000 0.0786 0.0000\n- per0 per0 per25 per25 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.620000 0.0786 0.0000\n- per0 per0 per26 per26 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.570000 0.0786 0.0000\n- per0 per0 per27 per27 UN NA 0.7134 0.2866 0.0000 0.1433 0 0.620000 0.0786 0.0000\n- per0 per0 per28 per28 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.580000 0.7603 NA\n- per0 per0 per29 per29 UN NA 0.4440 0.5560 0.0000 0.2780 0 0.670000 0.7603 NA\n- per0 per0 per30 per30 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.640000 0.0786 0.0000\n- per0 per0 per31 per31 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.610000 0.7603 NA\n- per0 per0 per32 per32 UN NA 0.7989 0.0411 0.1600 0.1806 0 0.690000 0.0786 0.0000\n- per0 per0 per33 per33 UN NA 0.8888 0.0000 0.1112 0.1112 -1 0.660000 0.7603 NA\n- per0 per0 per34 per34 UN NA 0.8561 0.1439 0.0000 0.0720 -1 0.600000 0.7603 NA\n- per0 per0 per35 per35 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.560000 0.0786 0.0000\n- per0 per0 per36 per36 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.630000 0.7603 NA\n- per0 per0 per37 per37 UN NA 0.6054 0.3946 0.0000 0.1973 0 0.570000 0.7603 NA\n- per0 per0 per38 per38 UN NA 0.9219 0.0781 0.0000 0.0391 0 0.620000 0.7603 NA\n- per0 per0 per39 per39 UN NA '..b'.8570 0.0000 0.1430 0.1430 -1 0.670000 0.7603 NA\n- per190 per190 per197 per197 UN NA 0.7134 0.2866 0.0000 0.1433 -1 0.620000 0.0786 0.0000\n- per190 per190 per198 per198 UN NA 0.4440 0.5560 0.0000 0.2780 -1 0.670000 0.7603 NA\n- per190 per190 per199 per199 UN NA 0.8570 0.0000 0.1430 0.1430 0 0.670000 0.7603 NA\n- per191 per191 per192 per192 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.610000 0.0786 0.0000\n- per191 per191 per193 per193 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.580000 0.0786 0.0000\n- per191 per191 per194 per194 UN NA 0.4282 0.5718 0.0000 0.2859 0 0.660000 0.0786 0.0000\n- per191 per191 per195 per195 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.550000 0.0786 0.0000\n- per191 per191 per196 per196 UN NA 0.6659 0.3341 0.0000 0.1670 -1 0.600000 0.0786 0.0000\n- per191 per191 per197 per197 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.590000 0.0786 0.0000\n- per191 per191 per198 per198 UN NA 0.4282 0.5718 0.0000 0.2859 -1 0.660000 0.0786 0.0000\n- per191 per191 per199 per199 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.600000 0.0786 0.0000\n- per192 per192 per193 per193 UN NA 0.7989 0.1210 0.0801 0.1406 0 0.670000 0.7603 NA\n- per192 per192 per194 per194 UN NA 0.6054 0.3946 0.0000 0.1973 0 0.570000 0.7603 NA\n- per192 per192 per195 per195 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.540000 0.7603 NA\n- per192 per192 per196 per196 UN NA 0.6391 0.2807 0.0802 0.2205 -1 0.690000 0.7603 NA\n- per192 per192 per197 per197 UN NA 0.3196 0.6400 0.0404 0.3604 -1 0.720000 0.7603 NA\n- per192 per192 per198 per198 UN NA 0.7399 0.2601 0.0000 0.1301 -1 0.630000 0.7603 NA\n- per192 per192 per199 per199 UN NA 0.2960 0.7040 0.0000 0.3520 0 0.690000 0.7603 NA\n- per193 per193 per194 per194 UN NA 0.9219 0.0781 0.0000 0.0391 1 0.620000 0.7603 NA\n- per193 per193 per195 per195 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.630000 0.7603 NA\n- per193 per193 per196 per196 UN NA 0.3996 0.6004 0.0000 0.3002 0 0.640000 0.7603 NA\n- per193 per193 per197 per197 UN NA 0.5511 0.4489 0.0000 0.2244 0 0.630000 0.7603 NA\n- per193 per193 per198 per198 UN NA 0.4611 0.5389 0.0000 0.2695 0 0.680000 0.7603 NA\n- per193 per193 per199 per199 UN NA 0.9219 0.0781 0.0000 0.0391 1 0.620000 0.7603 NA\n- per194 per194 per195 per195 UN NA 0.9587 0.0413 0.0000 0.0207 0 0.630000 0.7603 NA\n- per194 per194 per196 per196 UN NA 1.0000 0.0000 0.0000 0.0000 0 0.580000 0.7603 NA\n- per194 per194 per197 per197 UN NA 0.7399 0.2601 0.0000 0.1301 0 0.630000 0.7603 NA\n- per194 per194 per198 per198 UN NA 0.9587 0.0013 0.0400 0.0407 0 0.640000 0.7603 NA\n- per194 per194 per199 per199 UN NA 0.7683 0.2317 0.0000 0.1158 1 0.640000 0.7603 NA\n- per195 per195 per196 per196 UN NA 0.5919 0.4081 0.0000 0.2040 -1 0.650000 0.7603 NA\n- per195 per195 per197 per197 UN NA 1.0000 0.0000 0.0000 0.0000 -1 0.580000 0.0786 0.0000\n- 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 16d22eee0fe3 -r 272aca44b3dd test-data/stats.log --- a/test-data/stats.log Thu Dec 02 16:20:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,40 +0,0 @@ -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 |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/test2_out.bed |
| b |
| Binary file test-data/test2_out.bed has changed |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/test2_out.bim --- a/test-data/test2_out.bim Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/test2_out.bim Sun Dec 19 15:53:35 2021 +0000 |
| b |
| @@ -1,13 +1,13 @@ 1 snp0 0 0 A B 1 snp1 0 1 B A -1 snp2 0 2 B A -1 snp3 0 3 A B +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 B A -1 snp9 0 9 A B +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 @@ -17,13 +17,13 @@ 1 snp16 0 16 B A 1 snp17 0 17 B A 1 snp18 0 18 B A -1 snp19 0 19 A B +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 B A +1 snp23 0 23 A B 1 snp24 0 24 A B -1 snp25 0 25 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 @@ -35,17 +35,17 @@ 1 snp34 0 34 B A 1 snp35 0 35 B A 1 snp36 0 36 B A -1 snp37 0 37 A B +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 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 B A +1 snp47 0 47 A B 1 snp48 0 48 A B 1 snp49 0 49 B A 1 snp50 0 50 A B |
| b |
| diff -r 16d22eee0fe3 -r 272aca44b3dd test-data/test2_out.fam --- a/test-data/test2_out.fam Thu Dec 02 16:20:30 2021 +0000 +++ b/test-data/test2_out.fam Sun Dec 19 15:53:35 2021 +0000 |
| b |
| @@ -1,32 +1,32 @@ 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 +per2 per2 0 0 2 2 +per3 per3 0 0 2 2 +per4 per4 0 0 2 2 per5 per5 0 0 2 1 -per6 per6 0 0 2 2 +per6 per6 0 0 2 1 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 +per12 per12 0 0 2 2 per13 per13 0 0 2 2 per14 per14 0 0 2 2 -per15 per15 0 0 2 1 +per15 per15 0 0 2 2 per16 per16 0 0 2 2 -per17 per17 0 0 2 2 +per17 per17 0 0 2 1 per18 per18 0 0 2 1 -per19 per19 0 0 2 2 +per19 per19 0 0 2 1 per20 per20 0 0 2 2 per21 per21 0 0 2 2 -per22 per22 0 0 2 2 +per22 per22 0 0 2 1 per23 per23 0 0 2 2 -per24 per24 0 0 2 1 +per24 per24 0 0 2 2 per25 per25 0 0 2 1 per26 per26 0 0 2 2 -per27 per27 0 0 2 2 -per28 per28 0 0 2 2 +per27 per27 0 0 2 1 +per28 per28 0 0 2 1 per29 per29 0 0 2 2 per30 per30 0 0 2 2 per31 per31 0 0 2 2 @@ -34,62 +34,62 @@ per33 per33 0 0 2 1 per34 per34 0 0 2 1 per35 per35 0 0 2 1 -per36 per36 0 0 2 2 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