Rename 'svType' column to 'type'

Not all variants are necessarily 'SVs'
MarWoes · Oct 9, 2017 · 5151059 · 5151059
1 parent eba8d69
commit 5151059
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Showing 18 changed files with 22 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ These parameters act as input to the VIPER server and must be specified by the u
 
 | parameter | description |
 |-------| ----------- |
-| *analysisFile* | File containing variant calls (must be a `.csv` or `.vcf` file). `.csv` files must include a header with column names. Columns `sample`, `svType`, `chr1`, `bp1`, `chr2` and `bp2` are mandatory.
+| *analysisFile* | File containing variant calls (must be a `.csv` or `.vcf` file). `.csv` files must include a header with column names. Columns `sample`, `type`, `chr1`, `bp1`, `chr2` and `bp2` are mandatory.
 | *workDir* | Directory that stores images by igv and decision progress. **WARNING: Do not delete this directory, or your progress will be lost** |
 | *bamDir* | Directory containing your `.bam`/`.bai`  sample files. |
 

diff --git a/src/main/java/de/imi/marw/viper/variants/table/VariantTable.java b/src/main/java/de/imi/marw/viper/variants/table/VariantTable.java
@@ -37,7 +37,7 @@
  */
 public class VariantTable {
 
-    public static final String TYPE_COLUMN_NAME = "svType";
+    public static final String TYPE_COLUMN_NAME = "type";
     public static final String SAMPLE_COLUMN_NAME = "sample";
     public static final String CHR1_COLUMN_NAME = "chr1";
     public static final String CHR2_COLUMN_NAME = "chr2";

diff --git a/src/test/java/de/imi/marw/viper/test/variants/CallStringifierTest.java b/src/test/java/de/imi/marw/viper/test/variants/CallStringifierTest.java
@@ -41,7 +41,7 @@ public void callsAreCorrectlyTurnedIntoStrings() {
         VariantTable table = new CsvTableReader(';', ",").readTable(TestUtil.getResourceFile("examples-small.csv"));
 
         List<List<String>> expectedStrings = Arrays.asList(
-                Arrays.asList("sample", "svType", "chr1", "bp1", "chr2", "bp2", "strColl", "numColl", "naColl"),
+                Arrays.asList("sample", "type", "chr1", "bp1", "chr2", "bp2", "strColl", "numColl", "naColl"),
                 Arrays.asList("SAMPLE1", "DELETION", "X", "1000000", "X", "2000000", "hallo, huhu", "1", "NA"),
                 Arrays.asList("SAMPLE1", "DELETION", "1", "1000000", "1", "2000000", "blub", "1, 2, 3, 4", "NA"),
                 Arrays.asList("SAMPLE2", "DELETION", "2", "1000000", "2", "2000000", "NA", "NA", "NA"),

diff --git a/src/test/resources/api/expected-column-names.json b/src/test/resources/api/expected-column-names.json
@@ -2,7 +2,7 @@
 "viperId",
 "viperDecision",
 "sample",
-"svType",
+"type",
 "chr1",
 "bp1",
 "chr2",

diff --git a/src/test/resources/api/expected-first-row.json b/src/test/resources/api/expected-first-row.json
@@ -2,7 +2,7 @@
 "viperId":"VAR01",
 "viperDecision":"NA",
 "sample":["SIM1"],
-"svType":["DELETION"],
+"type":["DELETION"],
 "chr1":["1"],
 "bp1":3.6933582E7,
 "chr2":["1"],

diff --git a/src/test/resources/api/expected-related-calls.json b/src/test/resources/api/expected-related-calls.json
@@ -1,6 +1,6 @@
 [{
 "sample":"SIM1",
-"svType":"DELETION",
+"type":"DELETION",
 "chr1":"2",
 "bp1":2.5459763E7,
 "chr2":"2",
@@ -16,7 +16,7 @@
 "combinedValue":[null]
 },{
 "sample":"SIM1",
-"svType":"DELETION",
+"type":"DELETION",
 "chr1":"2",
 "bp1":2.5459763E7,
 "chr2":"2",
@@ -32,7 +32,7 @@
 "combinedValue":[null]
 },{
 "sample":"SIM1",
-"svType":"DELETION",
+"type":"DELETION",
 "chr1":"2",
 "bp1":2.5459764E7,
 "chr2":"2",

diff --git a/src/test/resources/api/expected-related-column-names.json b/src/test/resources/api/expected-related-column-names.json
@@ -1,6 +1,6 @@
 [
 "sample",
-"svType",
+"type",
 "chr1",
 "bp1",
 "chr2",

diff --git a/src/test/resources/api/expected-rows.json b/src/test/resources/api/expected-rows.json
@@ -2,7 +2,7 @@
 "viperId":"VAR02",
 "viperDecision":"NA",
 "sample":["SIM1"],
-"svType":["DELETION"],
+"type":["DELETION"],
 "chr1":["2"],
 "bp1":2.5459768E7,
 "chr2":["2"],
@@ -20,7 +20,7 @@
 "viperId":"VAR03",
 "viperDecision":"NA",
 "sample":["SIM1"],
-"svType":["DELETION"],
+"type":["DELETION"],
 "chr1":["2"],
 "bp1":2.5470618E7,
 "chr2":["2"],
@@ -38,7 +38,7 @@
 "viperId":"VAR04",
 "viperDecision":"NA",
 "sample":["SIM1"],
-"svType":["DELETION"],
+"type":["DELETION"],
 "chr1":["2"],
 "bp1":2.5459763E7,
 "chr2":["2"],

diff --git a/src/test/resources/examples-edge-cases.csv b/src/test/resources/examples-edge-cases.csv
@@ -1,2 +1,2 @@
-"sample"	"svType"	"chr1"	"bp1"	"chr2"	"bp2"	"strColl"	"numColl"
+"sample"	"type"	"chr1"	"bp1"	"chr2"	"bp2"	"strColl"	"numColl"
 " 	Åloha|öäüß##"	"DEL"	"MT"	"123"	"X"	"250"	"blub_ asdf"	"1,2,3"
diff --git a/src/test/resources/examples-empty.csv b/src/test/resources/examples-empty.csv
@@ -1 +1 @@
-sample;svType;chr1;bp1;chr2;bp2
+sample;type;chr1;bp1;chr2;bp2
diff --git a/src/test/resources/examples-filtering.csv b/src/test/resources/examples-filtering.csv
@@ -1,4 +1,4 @@
-viperId;sample;svType;chr1;bp1;chr2;bp2;strColl;numColl;num;str
+viperId;sample;type;chr1;bp1;chr2;bp2;strColl;numColl;num;str
 V1;SAMPLE4;DUPLICATION;2;100000010;2;100000110;NA;1;5;NA
 V2;SAMPLE1;DELETION;X;123000000;X;123000010;STR1,STR2;1,2,3,4;4;HALLO
 V3;SAMPLE2;TRANSLOCATION;1;19000000;2;20000000;NA;NA;3;NA

diff --git a/src/test/resources/examples-small.csv b/src/test/resources/examples-small.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;strColl;numColl;naColl
+sample;type;chr1;bp1;chr2;bp2;strColl;numColl;naColl
 SAMPLE1;DELETION;X;1000000;X;2000000;hallo,huhu;1;NA
 SAMPLE1;DELETION;1;1000000;1;2000000;blub;1,2,3,4;NA
 SAMPLE2;DELETION;2;1000000;2;2000000;NA;NA;NA

diff --git a/src/test/resources/examples-unclustered.csv b/src/test/resources/examples-unclustered.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;genes;na
+sample;type;chr1;bp1;chr2;bp2;genes;na
 SAMPLE4;DUPLICATION;2;100000010;2;100000110;GEN3;NA
 SAMPLE1;DELETION;X;123000000;X;123000010;NA;NA
 SAMPLE2;TRANSLOCATION;1;19000000;2;20000000;NA;NA

diff --git a/src/test/resources/examples.csv b/src/test/resources/examples.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;supporting;tool;genes;database;cov1;cov2;qual1;qual2;combinedValue
+sample;type;chr1;bp1;chr2;bp2;supporting;tool;genes;database;cov1;cov2;qual1;qual2;combinedValue
 SIM1;DELETION;1;36933582;1;36933621;10.0877192982;BreaKmer;CSF3R;NA;611.2222222222;358.987654321;35.0367205963;35.4265424032;NA
 SIM1;DELETION;1;36933582;1;36933621;26.1363636364;Pindel;CSF3R;NA;611.2222222222;358.987654321;35.0367205963;35.4265424032;NA
 SIM1;DELETION;2;25459763;2;25459832;36.2694300518;Socrates;DNMT3A;NA;1116.4691358025;2377.8024691358;35.3872216202;34.8203393527;NA

diff --git a/src/test/resources/vcf-import-complex-all.csv b/src/test/resources/vcf-import-complex-all.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER;INFO:NS;INFO:DP;INFO:AF;INFO:AA;INFO:DB;INFO:H2;FORMAT:GT;FORMAT:GQ;FORMAT:DP;FORMAT:HQ
+sample;type;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER;INFO:NS;INFO:DP;INFO:AF;INFO:AA;INFO:DB;INFO:H2;FORMAT:GT;FORMAT:GQ;FORMAT:DP;FORMAT:HQ
 NA00001;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS;3;14;0.5;NA;true;NA;G|G;48;1;51
 NA00002;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS;3;14;0.5;NA;true;NA;A|G;48;8;51
 NA00003;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS;3;14;0.5;NA;true;NA;A/A;43;5;NA

diff --git a/src/test/resources/vcf-import-complex-nonref.csv b/src/test/resources/vcf-import-complex-nonref.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER;INFO:NS;INFO:DP;INFO:AF;INFO:AA;INFO:DB;INFO:H2;FORMAT:GT;FORMAT:GQ;FORMAT:DP;FORMAT:HQ
+sample;type;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER;INFO:NS;INFO:DP;INFO:AF;INFO:AA;INFO:DB;INFO:H2;FORMAT:GT;FORMAT:GQ;FORMAT:DP;FORMAT:HQ
 NA00002;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS;3;14;0.5;NA;true;NA;A|G;48;8;51
 NA00003;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS;3;14;0.5;NA;true;NA;A/A;43;5;NA
 NA00002;SNP;20;17330;20;17330;NA;T;A;3;q10;3;11;0.017;NA;NA;NA;T|A;3;5;65, 3

diff --git a/src/test/resources/vcf-import-simple-all.csv b/src/test/resources/vcf-import-simple-all.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER
+sample;type;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER
 NA00001;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS
 NA00002;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS
 NA00003;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS

diff --git a/src/test/resources/vcf-import-simple-nonref.csv b/src/test/resources/vcf-import-simple-nonref.csv
@@ -1,4 +1,4 @@
-sample;svType;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER
+sample;type;chr1;bp1;chr2;bp2;ID;REF;ALT;QUAL;FILTER
 NA00002;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS
 NA00003;SNP;20;14370;20;14370;rs6054257;G;A;29;PASS
 NA00002;SNP;20;17330;20;17330;NA;T;A;3;q10
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		sample;svType;chr1;bp1;chr2;bp2
		sample;type;chr1;bp1;chr2;bp2