ngs_server 0.1 → 0.2
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- data/bin/ngs_server +72 -50
- data/ext/bamtools/extconf.rb +3 -3
- data/ext/vcftools/Makefile +28 -0
- data/ext/vcftools/README.txt +36 -0
- data/ext/vcftools/cpp/.svn/all-wcprops +125 -0
- data/ext/vcftools/cpp/.svn/dir-prop-base +6 -0
- data/ext/vcftools/cpp/.svn/entries +708 -0
- data/ext/vcftools/cpp/.svn/text-base/Makefile.svn-base +46 -0
- data/ext/vcftools/cpp/.svn/text-base/dgeev.cpp.svn-base +146 -0
- data/ext/vcftools/cpp/.svn/text-base/dgeev.h.svn-base +43 -0
- data/ext/vcftools/cpp/.svn/text-base/output_log.cpp.svn-base +79 -0
- data/ext/vcftools/cpp/.svn/text-base/output_log.h.svn-base +34 -0
- data/ext/vcftools/cpp/.svn/text-base/parameters.cpp.svn-base +535 -0
- data/ext/vcftools/cpp/.svn/text-base/parameters.h.svn-base +154 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_entry.cpp.svn-base +497 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_entry.h.svn-base +190 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_entry_getters.cpp.svn-base +421 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_entry_setters.cpp.svn-base +482 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file.cpp.svn-base +495 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file.h.svn-base +184 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file_diff.cpp.svn-base +1282 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file_filters.cpp.svn-base +1215 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file_format_convert.cpp.svn-base +1138 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file_index.cpp.svn-base +171 -0
- data/ext/vcftools/cpp/.svn/text-base/vcf_file_output.cpp.svn-base +3012 -0
- data/ext/vcftools/cpp/.svn/text-base/vcftools.cpp.svn-base +107 -0
- data/ext/vcftools/cpp/.svn/text-base/vcftools.h.svn-base +25 -0
- data/ext/vcftools/cpp/Makefile +46 -0
- data/ext/vcftools/cpp/dgeev.cpp +146 -0
- data/ext/vcftools/cpp/dgeev.h +43 -0
- data/ext/vcftools/cpp/output_log.cpp +79 -0
- data/ext/vcftools/cpp/output_log.h +34 -0
- data/ext/vcftools/cpp/parameters.cpp +535 -0
- data/ext/vcftools/cpp/parameters.h +154 -0
- data/ext/vcftools/cpp/vcf_entry.cpp +497 -0
- data/ext/vcftools/cpp/vcf_entry.h +190 -0
- data/ext/vcftools/cpp/vcf_entry_getters.cpp +421 -0
- data/ext/vcftools/cpp/vcf_entry_setters.cpp +482 -0
- data/ext/vcftools/cpp/vcf_file.cpp +495 -0
- data/ext/vcftools/cpp/vcf_file.h +184 -0
- data/ext/vcftools/cpp/vcf_file_diff.cpp +1282 -0
- data/ext/vcftools/cpp/vcf_file_filters.cpp +1215 -0
- data/ext/vcftools/cpp/vcf_file_format_convert.cpp +1138 -0
- data/ext/vcftools/cpp/vcf_file_index.cpp +171 -0
- data/ext/vcftools/cpp/vcf_file_output.cpp +3012 -0
- data/ext/vcftools/cpp/vcftools.cpp +107 -0
- data/ext/vcftools/cpp/vcftools.h +25 -0
- data/ext/vcftools/examples/.svn/all-wcprops +185 -0
- data/ext/vcftools/examples/.svn/dir-prop-base +6 -0
- data/ext/vcftools/examples/.svn/entries +1048 -0
- data/ext/vcftools/examples/.svn/prop-base/perl-api-1.pl.svn-base +5 -0
- data/ext/vcftools/examples/.svn/text-base/annotate-test.vcf.svn-base +37 -0
- data/ext/vcftools/examples/.svn/text-base/annotate.out.svn-base +23 -0
- data/ext/vcftools/examples/.svn/text-base/annotate.txt.svn-base +7 -0
- data/ext/vcftools/examples/.svn/text-base/annotate2.out.svn-base +52 -0
- data/ext/vcftools/examples/.svn/text-base/annotate3.out.svn-base +23 -0
- data/ext/vcftools/examples/.svn/text-base/cmp-test-a-3.3.vcf.svn-base +12 -0
- data/ext/vcftools/examples/.svn/text-base/cmp-test-a.vcf.svn-base +12 -0
- data/ext/vcftools/examples/.svn/text-base/cmp-test-b-3.3.vcf.svn-base +12 -0
- data/ext/vcftools/examples/.svn/text-base/cmp-test-b.vcf.svn-base +12 -0
- data/ext/vcftools/examples/.svn/text-base/cmp-test.out.svn-base +53 -0
- data/ext/vcftools/examples/.svn/text-base/concat-a.vcf.svn-base +21 -0
- data/ext/vcftools/examples/.svn/text-base/concat-b.vcf.svn-base +13 -0
- data/ext/vcftools/examples/.svn/text-base/concat-c.vcf.svn-base +19 -0
- data/ext/vcftools/examples/.svn/text-base/concat.out.svn-base +39 -0
- data/ext/vcftools/examples/.svn/text-base/invalid-4.0.vcf.svn-base +31 -0
- data/ext/vcftools/examples/.svn/text-base/isec-n2-test.vcf.out.svn-base +19 -0
- data/ext/vcftools/examples/.svn/text-base/merge-test-a.vcf.svn-base +17 -0
- data/ext/vcftools/examples/.svn/text-base/merge-test-b.vcf.svn-base +17 -0
- data/ext/vcftools/examples/.svn/text-base/merge-test-c.vcf.svn-base +15 -0
- data/ext/vcftools/examples/.svn/text-base/merge-test.vcf.out.svn-base +31 -0
- data/ext/vcftools/examples/.svn/text-base/perl-api-1.pl.svn-base +46 -0
- data/ext/vcftools/examples/.svn/text-base/query-test.out.svn-base +6 -0
- data/ext/vcftools/examples/.svn/text-base/shuffle-test.vcf.svn-base +12 -0
- data/ext/vcftools/examples/.svn/text-base/subset.SNPs.out.svn-base +10 -0
- data/ext/vcftools/examples/.svn/text-base/subset.indels.out.svn-base +18 -0
- data/ext/vcftools/examples/.svn/text-base/subset.vcf.svn-base +21 -0
- data/ext/vcftools/examples/.svn/text-base/valid-3.3.vcf.svn-base +30 -0
- data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.stats.svn-base +104 -0
- data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.svn-base +34 -0
- data/ext/vcftools/examples/.svn/text-base/valid-4.1.vcf.svn-base +37 -0
- data/ext/vcftools/examples/annotate-test.vcf +37 -0
- data/ext/vcftools/examples/annotate.out +23 -0
- data/ext/vcftools/examples/annotate.txt +7 -0
- data/ext/vcftools/examples/annotate2.out +52 -0
- data/ext/vcftools/examples/annotate3.out +23 -0
- data/ext/vcftools/examples/cmp-test-a-3.3.vcf +12 -0
- data/ext/vcftools/examples/cmp-test-a.vcf +12 -0
- data/ext/vcftools/examples/cmp-test-b-3.3.vcf +12 -0
- data/ext/vcftools/examples/cmp-test-b.vcf +12 -0
- data/ext/vcftools/examples/cmp-test.out +53 -0
- data/ext/vcftools/examples/concat-a.vcf +21 -0
- data/ext/vcftools/examples/concat-b.vcf +13 -0
- data/ext/vcftools/examples/concat-c.vcf +19 -0
- data/ext/vcftools/examples/concat.out +39 -0
- data/ext/vcftools/examples/invalid-4.0.vcf +31 -0
- data/ext/vcftools/examples/isec-n2-test.vcf.out +19 -0
- data/ext/vcftools/examples/merge-test-a.vcf +17 -0
- data/ext/vcftools/examples/merge-test-b.vcf +17 -0
- data/ext/vcftools/examples/merge-test-c.vcf +15 -0
- data/ext/vcftools/examples/merge-test.vcf.out +31 -0
- data/ext/vcftools/examples/perl-api-1.pl +46 -0
- data/ext/vcftools/examples/query-test.out +6 -0
- data/ext/vcftools/examples/shuffle-test.vcf +12 -0
- data/ext/vcftools/examples/subset.SNPs.out +10 -0
- data/ext/vcftools/examples/subset.indels.out +18 -0
- data/ext/vcftools/examples/subset.vcf +21 -0
- data/ext/vcftools/examples/valid-3.3.vcf +30 -0
- data/ext/vcftools/examples/valid-4.0.vcf +34 -0
- data/ext/vcftools/examples/valid-4.0.vcf.stats +104 -0
- data/ext/vcftools/examples/valid-4.1.vcf +37 -0
- data/ext/vcftools/extconf.rb +2 -0
- data/ext/vcftools/perl/.svn/all-wcprops +149 -0
- data/ext/vcftools/perl/.svn/entries +844 -0
- data/ext/vcftools/perl/.svn/prop-base/fill-aa.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/fill-an-ac.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/fill-ref-md5.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/tab-to-vcf.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/test.t.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-annotate.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-compare.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-concat.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-convert.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-fix-newlines.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-isec.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-merge.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-query.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-shuffle-cols.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-sort.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-stats.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-subset.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-to-tab.svn-base +5 -0
- data/ext/vcftools/perl/.svn/prop-base/vcf-validator.svn-base +5 -0
- data/ext/vcftools/perl/.svn/text-base/ChangeLog.svn-base +84 -0
- data/ext/vcftools/perl/.svn/text-base/FaSlice.pm.svn-base +214 -0
- data/ext/vcftools/perl/.svn/text-base/Makefile.svn-base +12 -0
- data/ext/vcftools/perl/.svn/text-base/Vcf.pm.svn-base +2853 -0
- data/ext/vcftools/perl/.svn/text-base/VcfStats.pm.svn-base +681 -0
- data/ext/vcftools/perl/.svn/text-base/fill-aa.svn-base +103 -0
- data/ext/vcftools/perl/.svn/text-base/fill-an-ac.svn-base +56 -0
- data/ext/vcftools/perl/.svn/text-base/fill-ref-md5.svn-base +204 -0
- data/ext/vcftools/perl/.svn/text-base/tab-to-vcf.svn-base +92 -0
- data/ext/vcftools/perl/.svn/text-base/test.t.svn-base +376 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-annotate.svn-base +1099 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-compare.svn-base +1193 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-concat.svn-base +310 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-convert.svn-base +180 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-fix-newlines.svn-base +97 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-isec.svn-base +660 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-merge.svn-base +577 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-query.svn-base +272 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-shuffle-cols.svn-base +89 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-sort.svn-base +79 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-stats.svn-base +160 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-subset.svn-base +206 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-to-tab.svn-base +112 -0
- data/ext/vcftools/perl/.svn/text-base/vcf-validator.svn-base +145 -0
- data/ext/vcftools/perl/ChangeLog +84 -0
- data/ext/vcftools/perl/FaSlice.pm +214 -0
- data/ext/vcftools/perl/Makefile +12 -0
- data/ext/vcftools/perl/Vcf.pm +2853 -0
- data/ext/vcftools/perl/VcfStats.pm +681 -0
- data/ext/vcftools/perl/fill-aa +103 -0
- data/ext/vcftools/perl/fill-an-ac +56 -0
- data/ext/vcftools/perl/fill-ref-md5 +204 -0
- data/ext/vcftools/perl/tab-to-vcf +92 -0
- data/ext/vcftools/perl/test.t +376 -0
- data/ext/vcftools/perl/vcf-annotate +1099 -0
- data/ext/vcftools/perl/vcf-compare +1193 -0
- data/ext/vcftools/perl/vcf-concat +310 -0
- data/ext/vcftools/perl/vcf-convert +180 -0
- data/ext/vcftools/perl/vcf-fix-newlines +97 -0
- data/ext/vcftools/perl/vcf-isec +660 -0
- data/ext/vcftools/perl/vcf-merge +577 -0
- data/ext/vcftools/perl/vcf-query +286 -0
- data/ext/vcftools/perl/vcf-shuffle-cols +89 -0
- data/ext/vcftools/perl/vcf-sort +79 -0
- data/ext/vcftools/perl/vcf-stats +160 -0
- data/ext/vcftools/perl/vcf-subset +206 -0
- data/ext/vcftools/perl/vcf-to-tab +112 -0
- data/ext/vcftools/perl/vcf-validator +145 -0
- data/ext/vcftools/website/.svn/all-wcprops +41 -0
- data/ext/vcftools/website/.svn/entries +238 -0
- data/ext/vcftools/website/.svn/prop-base/VCF-poster.pdf.svn-base +5 -0
- data/ext/vcftools/website/.svn/prop-base/favicon.ico.svn-base +5 -0
- data/ext/vcftools/website/.svn/prop-base/favicon.png.svn-base +5 -0
- data/ext/vcftools/website/.svn/text-base/Makefile.svn-base +6 -0
- data/ext/vcftools/website/.svn/text-base/README.svn-base +2 -0
- data/ext/vcftools/website/.svn/text-base/VCF-poster.pdf.svn-base +0 -0
- data/ext/vcftools/website/.svn/text-base/default.css.svn-base +250 -0
- data/ext/vcftools/website/.svn/text-base/favicon.ico.svn-base +0 -0
- data/ext/vcftools/website/.svn/text-base/favicon.png.svn-base +0 -0
- data/ext/vcftools/website/Makefile +6 -0
- data/ext/vcftools/website/README +2 -0
- data/ext/vcftools/website/VCF-poster.pdf +0 -0
- data/ext/vcftools/website/default.css +250 -0
- data/ext/vcftools/website/favicon.ico +0 -0
- data/ext/vcftools/website/favicon.png +0 -0
- data/ext/vcftools/website/img/.svn/all-wcprops +53 -0
- data/ext/vcftools/website/img/.svn/entries +300 -0
- data/ext/vcftools/website/img/.svn/prop-base/bg.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/bgcode.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/bgcontainer.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/bgul.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/header.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/li.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/quote.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/prop-base/search.gif.svn-base +5 -0
- data/ext/vcftools/website/img/.svn/text-base/bg.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/bgcode.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/bgcontainer.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/bgul.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/header.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/li.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/quote.gif.svn-base +0 -0
- data/ext/vcftools/website/img/.svn/text-base/search.gif.svn-base +0 -0
- data/ext/vcftools/website/img/bg.gif +0 -0
- data/ext/vcftools/website/img/bgcode.gif +0 -0
- data/ext/vcftools/website/img/bgcontainer.gif +0 -0
- data/ext/vcftools/website/img/bgul.gif +0 -0
- data/ext/vcftools/website/img/header.gif +0 -0
- data/ext/vcftools/website/img/li.gif +0 -0
- data/ext/vcftools/website/img/quote.gif +0 -0
- data/ext/vcftools/website/img/search.gif +0 -0
- data/ext/vcftools/website/src/.svn/all-wcprops +53 -0
- data/ext/vcftools/website/src/.svn/entries +300 -0
- data/ext/vcftools/website/src/.svn/text-base/docs.inc.svn-base +202 -0
- data/ext/vcftools/website/src/.svn/text-base/index.inc.svn-base +52 -0
- data/ext/vcftools/website/src/.svn/text-base/index.php.svn-base +80 -0
- data/ext/vcftools/website/src/.svn/text-base/license.inc.svn-base +27 -0
- data/ext/vcftools/website/src/.svn/text-base/links.inc.svn-base +13 -0
- data/ext/vcftools/website/src/.svn/text-base/options.inc.svn-base +654 -0
- data/ext/vcftools/website/src/.svn/text-base/perl_module.inc.svn-base +249 -0
- data/ext/vcftools/website/src/.svn/text-base/specs.inc.svn-base +18 -0
- data/ext/vcftools/website/src/docs.inc +202 -0
- data/ext/vcftools/website/src/index.inc +52 -0
- data/ext/vcftools/website/src/index.php +80 -0
- data/ext/vcftools/website/src/license.inc +27 -0
- data/ext/vcftools/website/src/links.inc +13 -0
- data/ext/vcftools/website/src/options.inc +654 -0
- data/ext/vcftools/website/src/perl_module.inc +249 -0
- data/ext/vcftools/website/src/specs.inc +18 -0
- data/lib/config.ru +9 -0
- data/lib/ngs_server/add.rb +9 -0
- data/lib/ngs_server/version.rb +1 -1
- data/lib/ngs_server.rb +55 -3
- data/ngs_server.gemspec +5 -2
- metadata +296 -6
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/*#############################################################
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Name: Transparentia
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Date: 2006-08-20
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Description: Simple, lightweight and slightly blue.
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Author: Viktor Persson
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URL: http://templates.arcsin.se
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Feel free to use and modify but please provide credits.
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#############################################################*/
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/* standard elements */
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* {
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margin: 0;
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padding: 0;
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a {
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color: #36C;
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}
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a:hover {
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color: #06F;
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}
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body {
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background: #EEE url(img/bg.gif);
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color: #444;
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/*font: normal 62.5% "Lucida Sans Unicode",sans-serif;*/
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font: normal 75% "Lucida Sans Unicode",sans-serif;
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margin: 0;
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}
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input {
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color: #555;
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font: normal 1.1em "Lucida Sans Unicode",sans-serif;
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}
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p,cite,code {
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h1 {
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font-size: 1.4em;
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margin-bottom: 6px;
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li {
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code {
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background: url(img/bgcode.gif);
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border: 1px solid #F0F0F0;
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border-left: 6px solid #39F;
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color: #555;
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display: block;
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font: normal 1.1em "Lucida Sans Unicode",serif;
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margin-bottom: 12px;
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padding: 8px 10px;
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