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Added gmql language definition
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‎demo/kitchen-sink/docs/gmql.gmql

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AAA_RAW = SELECT(cell == '[Cell_Name]' AND antibody_target == 'AAA' AND dataType == 'ChipSeq') HG19_ENCODE_BED;
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AAA_Cover_2 = COVER(2,ANY) AAA_RAW;
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BBB_RAW = SELECT(cell == '[Cell_Name]' AND antibody_target == 'BBB' AND dataType == 'ChipSeq') HG19_ENCODE_BED;
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BBB_Cover_2 = COVER(2,ANY) BBB_RAW;
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TSS = SELECT(annotation_type == 'TSS' AND provider == "UCSC") HG19_BED_ANNOTATION;
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TSS_AAA_2_L = JOIN(DLE(100000),UP; output: LEFT) TSS AAA_Cover_2;
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TSS_AAA_2_COUNT = MAP() TSS TSS_AAA_2_L;
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TSS_AAA_2_COUNT_0 = SELECT(region: count_TSS_TSS_AAA_2_L>0) TSS_AAA_2_COUNT;
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TSS_BBB_2_L = JOIN(DLE(100000),UP;output: LEFT) TSS BBB_Cover_2;
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TSS_BBB_2_COUNT = MAP() TSS TSS_BBB_2_L;
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TSS_BBB_2_COUNT_0 = SELECT(region: count_TSS_TSS_BBB_2_L>0) TSS_BBB_2_COUNT;
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COMMON_TSS = JOIN(DISTANCE<1;output: INT) TSS_AAA_2_COUNT_0 TSS_BBB_2_COUNT_0 ; # Under the hyphothesis (To Be Verified) that there are no partially overlapping TSSes
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# Doing this I skip the names. So I map again one of them of this to extract the names
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COMMON_TSS_NAMES = MAP() TSS COMMON_TSS;
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TSS_0 = SELECT(region: count_TSS_COMMON_TSS>0) COMMON_TSS_NAMES; # These are the common TSSes. Old name: COMMON_TSS_NAMES
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LONG_TSS_0 = PROJECT(region_modifier: left AS start - 100000) TSS_0; # Extend the TSSes
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TSS_0_AAA_2_CLOSE_0 = MAP(TSSname AS BAG($0)) AAA_Cover_2 LONG_TSS_0; # find the TFBS that are close on left to TSSes
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TSS_0_AAA_2_CLOSE = SELECT(region: count_AAA_Cover_2_LONG_TSS_0 > 0) TSS_0_AAA_2_CLOSE_0; # take out the irrelevant ones
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TSS_0_AAA_2_CLOSEST = JOIN(MD(1);output: LEFT) TSS_0_AAA_2_CLOSE TSS_0; # Find the closest TFBS
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TSS_0_BBB_2_CLOSE_0 = MAP(TSSname AS BAG($0)) BBB_Cover_2 LONG_TSS_0; # find the TFBS that are close on left to TSSes
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TSS_0_BBB_2_CLOSE = SELECT(region: count_BBB_Cover_2_LONG_TSS_0 > 0) TSS_0_BBB_2_CLOSE_0; # take out the irrelevant ones
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TSS_0_BBB_2_CLOSEST = JOIN(MD(1);output: LEFT) TSS_0_BBB_2_CLOSE TSS_0; # Find the closest TFBS
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MATERIALIZE TSS_0 into AAA_2_BBB_2_tss_0;
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MATERIALIZE TSS_0_AAA_2_CLOSEST into tss_0_AAA_2_closest;
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MATERIALIZE TSS_0_BBB_2_CLOSEST into tss_0_BBB_2_closest;

‎lib/ace/ext/modelist.js

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Gherkin: ["feature"],
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Gitignore: ["^.gitignore"],
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Glsl: ["glsl|frag|vert"],
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GMQL: ["gmql"],
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Gobstones: ["gbs"],
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golang: ["go"],
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Groovy: ["groovy"],

‎lib/ace/mode/gmql.js

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/* ***** BEGIN LICENSE BLOCK *****
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* Distributed under the BSD license:
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*
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* Copyright (c) 2010, Ajax.org B.V.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* documentation and/or other materials provided with the distribution.
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* * Neither the name of Ajax.org B.V. nor the
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* names of its contributors may be used to endorse or promote products
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* derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL AJAX.ORG B.V. BE LIABLE FOR ANY
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* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*
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* ***** END LICENSE BLOCK ***** */
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define(function(require, exports, module) {
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"use strict";
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var oop = require("../lib/oop");
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var TextMode = require("./text").Mode;
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var GmqlHighlightRules = require("./gmql_highlight_rules").GmqlHighlightRules;
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var Range = require("../range").Range;
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var Mode = function() {
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this.HighlightRules = GmqlHighlightRules;
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};
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oop.inherits(Mode, TextMode);
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(function() {
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this.lineCommentStart = "--";
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this.$id = "ace/mode/gmql";
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}).call(Mode.prototype);
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exports.Mode = Mode;
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});

‎lib/ace/mode/gmql_highlight_rules.js

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/* ***** BEGIN LICENSE BLOCK *****
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* Distributed under the BSD license:
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*
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* Copyright (c) 2010, Ajax.org B.V.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* documentation and/or other materials provided with the distribution.
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* * Neither the name of Ajax.org B.V. nor the
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* names of its contributors may be used to endorse or promote products
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* derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL AJAX.ORG B.V. BE LIABLE FOR ANY
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* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*
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* ***** END LICENSE BLOCK ***** */
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define(function(require, exports, module) {
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"use strict";
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var oop = require("../lib/oop");
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var TextHighlightRules = require("./text_highlight_rules").TextHighlightRules;
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var GmqlHighlightRules = function() {
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var keywords = (
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"select|project|extend|group|merge|order" //relational unary operations
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+ "|sort" // ?do we have? //relational unary operations
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+ "|union|difference" //relational binary operations
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+ "|cover|flat|summit|histogram|map|join" //domain specific operations
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+ "|materialize" //utility operations
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);
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var builtinConstants = (
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"true|false|distance|mindist|mindistance|dle|dge|md|any|all|start|stop|chr|strand|left|right|up|down|downstream|upstream"
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+ "|and|or|not|as|in|allbut"
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+ "|count|bag|sum|avg|min|max|median|std"
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+ "|cat|contig"
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);
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var builtinFunctions = (
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"region|semijoin" // SELECT
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+ "|metadata|region_update|metadata_update" // PROJECT
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+ "|meta_aggregate|region_group|region_aggregate" //GROUP
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+ "|groupby" // MERGE
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+ "|desc|meta_top|meta_topg|region_order|region_top|region_topg|" // ORDER
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+ "|groupby" // MERGE
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+ "|joinby" //DIFFERENCE
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+ "|aggregate" //COVER(flat/summit/histogram
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+ "|output" //JOIN
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+ "|into" //MATERIALIZE
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//+ "|parser|region_modifier|meta_modifier|meta_project"
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);
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var dataTypes = (
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"int|numeric|decimal|date|varchar|char|bigint|float|double|bit|binary|text|set|timestamp|" +
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"money|real|number|integer"
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);
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var keywordMapper = this.createKeywordMapper({
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"support.function": builtinFunctions,
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"keyword": keywords,
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"constant.language": builtinConstants,
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"storage.type": dataTypes
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}, "identifier", true);
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this.$rules = {
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"start" : [ {
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token : "comment",
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regex : "#.*$"
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}, {
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token : "string", // " string
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regex : '".*?"'
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}, {
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token : "string", // ' string
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regex : "'.*?'"
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}, {
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token : "constant.numeric", // float
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regex : "[+-]?\\d+(?:(?:\\.\\d*)?(?:[eE][+-]?\\d+)?)?\\b"
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}, {
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token : keywordMapper,
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regex : "[a-zA-Z_$][a-zA-Z0-9_$]*\\b"
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}, {
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token : "keyword.operator",
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regex : "\\+|\\-|\\/|\\/\\/|%|<@>|@>|<@|&|\\^|~|<|>|<=|=>|==|!=|<>|=|,|;|:"
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}, {
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token : "paren.lparen",
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regex : "[\\(]"
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}, {
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token : "paren.rparen",
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regex : "[\\)]"
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}, {
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token : "text",
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regex : "\\s+"
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} ]
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};
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this.normalizeRules();
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};
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oop.inherits(GmqlHighlightRules, TextHighlightRules);
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exports.GmqlHighlightRules = GmqlHighlightRules;
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});
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‎lib/ace/snippets/gmql.js

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define(function(require, exports, module) {
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"use strict";
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exports.snippetText = require("../requirejs/text!./gmql.snippets");
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exports.scope = "gmql";
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});

‎lib/ace/snippets/gmql.snippets

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##
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## SELECT
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snippet SELECT
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SELECT(${1:pm}; region: ${2:pr}; semijoin: ${3:psj(DSext)}) ${4:DSin};
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##
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## MATERIALIZE
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snippet MATERIALIZE
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MATERIALIZE ${1:DS} INTO ​${2:fileName};
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##
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## PROJECT
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snippet PROJECT
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PROJECT(region_update: ${1:new_right} AS ${2:right}) ${3:DS};
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##
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## EXTEND
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snippet EXTEND
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EXTEND(${1:RegionCount} AS COUNT()) ${2:EXP};
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##
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## GROUP
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snippet GROUP
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GROUP(${1:Tumor_type}; region_aggregate: ${2:Min AS MIN(score)}) ${3:EXP};
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##
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## ORDER
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snippet ORDER
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ORDER(Region_count ${1:DESC}; meta_top: ${2:2};) ${3:INPUT_DS};
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##
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## MERGE
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snippet MERGE
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MERGE(groupby: ${1:antibody_target}) ${2:EXPERIMENT};
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##
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## UNION
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snippet UNION
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UNION() ${1:BROAD} ${2:NARROW};
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##
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## DIFFERENCE
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snippet DIFFERENCE
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DIFFERENCE(joinby: ${1:antibody_target}) ${2:EXP1} ${3:EXP2};
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##
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## MAP
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snippet MAP
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MAP (${1:minScore} AS ${2:MIN(score)}; joinby: ${3:cell_tissue}) ${4:REF} ${5:EXP};
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##
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## JOIN
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snippet JOIN
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JOIN(${1:genometric_predicate}; output: ${2:CAT}; joinby: ${3:provider}) ${4:DS_ANCHOR} ${5:DS_EXP};
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##
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## COVER
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snippet COVER
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COVER(${1:minAcc}, ${2:maxAcc};​ groupby: ${3:cell}; aggregate: ${4:min_pValue} AS ${5:MIN(pValue)}) ${6:DSin};
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##
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## FLAT
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snippet FLAT
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FLAT(${1:minAcc}, ${2:maxAcc}; groupby: ${3:cell}) ${4:EXP};
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##
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## SUMMIT
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snippet SUMMIT
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SUMMIT(${1:minAcc}, ${2:maxAcc}; groupby: ${3:cell}) ${4:EXP};
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##
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## HISTOGRAM
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kerufherifuh
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snippet HISTOGRAM
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HISTOGRAM(${1:minAcc}, ${2:maxAcc}; groupby: ${3:cell}) ${4:EXP};
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##

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