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changed IS_GERMLINE to SV_STATUS
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@mandawilson
mandawilson committed Feb 8, 2022
1 parent e55e602 commit 32cbbb9
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Showing 17 changed files with 121 additions and 122 deletions.
7 changes: 3 additions & 4 deletions core/src/main/java/org/mskcc/cbio/portal/dao/DaoStructuralVariant.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ public static void addStructuralVariantToBulkLoader(StructuralVariant structural
"LENGTH",
"COMMENTS",
"EXTERNAL_ANNOTATION",
"IS_GERMLINE",
"SV_STATUS",
};
bl.setFieldNames(fieldNames);

Expand Down Expand Up @@ -123,8 +123,7 @@ public static void addStructuralVariantToBulkLoader(StructuralVariant structural
Integer.toString(structuralVariant.getLength()),
structuralVariant.getComments(),
structuralVariant.getExternalAnnotation(),
Integer.toString(structuralVariant.getIsGermline()?1:0));
//TODO: fix this ... the value must be converted to an integer
structuralVariant.getSvStatus());

if ((structuralVariant.getDriverFilter() != null
&& !structuralVariant.getDriverFilter().isEmpty()
Expand Down Expand Up @@ -240,7 +239,7 @@ private static StructuralVariant extractStructuralVariant(ResultSet rs) throws S
structuralVariant.setDriverFilterAnn(rs.getString("DRIVER_FILTER_ANNOTATION"));
structuralVariant.setDriverTiersFilter(rs.getString("DRIVER_TIERS_FILTER"));
structuralVariant.setDriverTiersFilterAnn(rs.getString("DRIVER_TIERS_FILTER_ANNOTATION"));
structuralVariant.setIsGermline(rs.getBoolean("IS_GERMLINE"));
structuralVariant.setSvStatus(rs.getString("SV_STATUS"));
return structuralVariant;
}
}
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10 changes: 5 additions & 5 deletions core/src/main/java/org/mskcc/cbio/portal/model/StructuralVariant.java
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Expand Up @@ -69,7 +69,7 @@ public class StructuralVariant {
private String driverFilterAnn;
private String driverTiersFilter;
private String driverTiersFilterAnn;
private Boolean isGermline;
private String svStatus;

public long getInternalId() {
return internalId;
Expand Down Expand Up @@ -335,10 +335,10 @@ public String getDriverTiersFilterAnn() {
public void setDriverTiersFilterAnn(String driverTiersFilterAnn) {
this.driverTiersFilterAnn = driverTiersFilterAnn;
}
public Boolean getIsGermline() {
return isGermline;
public String getSvStatus() {
return svStatus;
}
public void setIsGermline(Boolean isGermline) {
this.isGermline = isGermline;
public void setSvStatus(String svStatus) {
this.svStatus = svStatus;
}
}
6 changes: 3 additions & 3 deletions core/src/main/java/org/mskcc/cbio/portal/util/StructuralVariantUtil.java
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Expand Up @@ -83,8 +83,8 @@ public class StructuralVariantUtil {
public static final String DRIVER_FILTER_ANNOTATION = "cbp_driver_annotation";
public static final String DRIVER_TIERS_FILTER = "cbp_driver_tiers";
public static final String DRIVER_TIERS_FILTER_ANNOTATION = "cbp_driver_tiers_annotation";
public static final String IS_GERMLINE = "is_germline";

public static final String SV_STATUS = "Sv_Status";
public StructuralVariantUtil(){}

public StructuralVariantUtil(String line) {
Expand Down Expand Up @@ -140,7 +140,7 @@ public StructuralVariant parseStructuralVariantRecord(String[] parts) {
structuralVariant.setDriverFilterAnn(TabDelimitedFileUtil.getPartString(getColumnIndex(StructuralVariantUtil.DRIVER_FILTER_ANNOTATION), parts));
structuralVariant.setDriverTiersFilter(TabDelimitedFileUtil.getPartString(getColumnIndex(StructuralVariantUtil.DRIVER_TIERS_FILTER), parts));
structuralVariant.setDriverTiersFilterAnn(TabDelimitedFileUtil.getPartString(getColumnIndex(StructuralVariantUtil.DRIVER_TIERS_FILTER_ANNOTATION), parts));
structuralVariant.setIsGermline(TabDelimitedFileUtil.getPartInt(getColumnIndex(StructuralVariantUtil.IS_GERMLINE), parts) != 0);
structuralVariant.setSvStatus(TabDelimitedFileUtil.getPartString(getColumnIndex(StructuralVariantUtil.SV_STATUS), parts));
return structuralVariant;
}

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6 changes: 3 additions & 3 deletions core/src/test/resources/data_structural_variants.txt
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@@ -1,3 +1,3 @@
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Ensembl_Transcript_Id Site1_Exon Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Ensembl_Transcript_Id Site2_Exon Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation is_germline
TCGA-A1-A0SB-01 NA KIAA1549 ENST00000242365 15 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF ENST00000288602 10 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA 0
TCGA-A1-A0SD-01 NA EML4 ENST00000318522 13 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK ENST00000389048 20 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA 0
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Ensembl_Transcript_Id Site1_Exon Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Ensembl_Transcript_Id Site2_Exon Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation Sv_Status
TCGA-A1-A0SB-01 NA KIAA1549 ENST00000242365 15 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF ENST00000288602 10 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA SOMATIC
TCGA-A1-A0SD-01 NA EML4 ENST00000318522 13 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK ENST00000389048 20 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA SOMATIC
16 changes: 8 additions & 8 deletions core/src/test/scripts/test_data/data_structural_variants_exon_not_in_transcript.txt
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@@ -1,8 +1,8 @@
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Ensembl_Transcript_Id Site1_Exon Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Ensembl_Transcript_Id Site2_Exon Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation is_germline
TCGA-A2-A04P-01 NA KIAA1549 ENST00000242365 1500 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF ENST00000288602 10 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA 0
TCGA-A2-A04P-01 NA NCOA4 ENST00000344348 7 10 51582939 NCOA4-RET.N7R12_1 NA RET ENST00000340058 12 10 43612031 NCOA4-RET.N7R12_2 NA GRCh37 no yes NA 1001 NA 800 NA NA NA NA NCOA4-RET.N7R1 NA NA NA Fusion NA NA Gain-of-Function NA NA NA NA NA 0
TCGA-A2-A04P-01 NA EML4 ENST00000318522 6 2 42492091 EML4-ALK.E6bA20.AB374362_1 NA ALK ENST00000389048 2000 2 29446394 EML4-ALK.E6bA20.AB374362_2 NA GRCh37 no yes NA 1002 NA 700 NA NA NA NA EML4-ALK.E6bA20.AB374362 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB374362 NA NA NA NA 0
TCGA-A2-A04P-01 NA TMPRSS2 ENST00000332149 1 21 42880007 TMPRSS2-ERG.T1E2.COSF23.1_1 NA ERG ENST00000442448 2 21 39956869 TMPRSS2-ERG.T1E2.COSF23.1_2 NA GRCh37 no yes NA 1003 NA 600 NA NA NA NA TMPRSS2-ERG.T1E2.COSF23.1 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF23 NA NA NA NA 0
TCGA-A2-A04P-01 NA EGFR ENST00000275493 1 7 55087058 EGFR-EGFR.E1E8.DelPositive.1_1 NA EGFR ENST00000275493 8 7 55223522 EGFR-EGFR.E1E8.DelPositive.1_2 NA GRCh37 no yes NA 1004 NA 500 NA NA NA NA EGFR-EGFR.E1E8.DelPositive NA NA NA Fusion NA NA NA NA NA NA NA NA 0
TCGA-A2-A04P-01 NA ALK ENST00000389048 11 2 29497964 ALK-PTPN3.A11P3_1 NA PTPN3 ENST00000374541 3 9 112219679 ALK-PTPN3.A11P3_2 NA GRCh37 no yes NA 1005 NA 400 NA NA NA NA ALK-PTPN3.A11P3 NA NA NA Fusion NA NA NA NA NA NA NA NA 0
TCGA-A1-A0SB-01 NA EML4 ENST00000318522 13 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK ENST00000389048 20 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA 0
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Ensembl_Transcript_Id Site1_Exon Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Ensembl_Transcript_Id Site2_Exon Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation Sv_Status
TCGA-A2-A04P-01 NA KIAA1549 ENST00000242365 1500 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF ENST00000288602 10 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA NCOA4 ENST00000344348 7 10 51582939 NCOA4-RET.N7R12_1 NA RET ENST00000340058 12 10 43612031 NCOA4-RET.N7R12_2 NA GRCh37 no yes NA 1001 NA 800 NA NA NA NA NCOA4-RET.N7R1 NA NA NA Fusion NA NA Gain-of-Function NA NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA EML4 ENST00000318522 6 2 42492091 EML4-ALK.E6bA20.AB374362_1 NA ALK ENST00000389048 2000 2 29446394 EML4-ALK.E6bA20.AB374362_2 NA GRCh37 no yes NA 1002 NA 700 NA NA NA NA EML4-ALK.E6bA20.AB374362 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB374362 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA TMPRSS2 ENST00000332149 1 21 42880007 TMPRSS2-ERG.T1E2.COSF23.1_1 NA ERG ENST00000442448 2 21 39956869 TMPRSS2-ERG.T1E2.COSF23.1_2 NA GRCh37 no yes NA 1003 NA 600 NA NA NA NA TMPRSS2-ERG.T1E2.COSF23.1 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF23 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA EGFR ENST00000275493 1 7 55087058 EGFR-EGFR.E1E8.DelPositive.1_1 NA EGFR ENST00000275493 8 7 55223522 EGFR-EGFR.E1E8.DelPositive.1_2 NA GRCh37 no yes NA 1004 NA 500 NA NA NA NA EGFR-EGFR.E1E8.DelPositive NA NA NA Fusion NA NA NA NA NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA ALK ENST00000389048 11 2 29497964 ALK-PTPN3.A11P3_1 NA PTPN3 ENST00000374541 3 9 112219679 ALK-PTPN3.A11P3_2 NA GRCh37 no yes NA 1005 NA 400 NA NA NA NA ALK-PTPN3.A11P3 NA NA NA Fusion NA NA NA NA NA NA NA NA SOMATIC
TCGA-A1-A0SB-01 NA EML4 ENST00000318522 13 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK ENST00000389048 20 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA SOMATIC
16 changes: 8 additions & 8 deletions core/src/test/scripts/test_data/data_structural_variants_missing_columns.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation is_germline
TCGA-A2-A04P-01 NA KIAA1549 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA 0
TCGA-A2-A04P-01 NA NCOA4 10 51582939 NCOA4-RET.N7R12_1 NA RET 10 43612031 NCOA4-RET.N7R12_2 NA GRCh37 no yes NA 1001 NA 800 NA NA NA NA NCOA4-RET.N7R1 NA NA NA Fusion NA NA Gain-of-Function NA NA NA NA NA 0
TCGA-A2-A04P-01 NA EML4 2 42492091 EML4-ALK.E6bA20.AB374362_1 NA ALK 2 29446394 EML4-ALK.E6bA20.AB374362_2 NA GRCh37 no yes NA 1002 NA 700 NA NA NA NA EML4-ALK.E6bA20.AB374362 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB374362 NA NA NA NA 0
TCGA-A2-A04P-01 NA TMPRSS2 21 42880007 TMPRSS2-ERG.T1E2.COSF23.1_1 NA ERG 21 39956869 TMPRSS2-ERG.T1E2.COSF23.1_2 NA GRCh37 no yes NA 1003 NA 600 NA NA NA NA TMPRSS2-ERG.T1E2.COSF23.1 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF23 NA NA NA NA 0
TCGA-A2-A04P-01 NA EGFR 7 55087058 EGFR-EGFR.E1E8.DelPositive.1_1 NA EGFR 7 55223522 EGFR-EGFR.E1E8.DelPositive.1_2 NA GRCh37 no yes NA 1004 NA 500 NA NA NA NA EGFR-EGFR.E1E8.DelPositive NA NA NA Fusion NA NA NA NA NA NA NA NA 0
TCGA-A2-A04P-01 NA ALK 2 29497964 ALK-PTPN3.A11P3_1 NA PTPN3 9 112219679 ALK-PTPN3.A11P3_2 NA GRCh37 no yes NA 1005 NA 400 NA NA NA NA ALK-PTPN3.A11P3 NA NA NA Fusion NA NA NA NA NA NA NA NA 0
TCGA-A1-A0SB-01 NA EML4 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA 0
Sample_ID Site1_Entrez_Gene_Id Site1_Hugo_Symbol Site1_Chromosome Site1_Position Site1_Description Site2_Entrez_Gene_Id Site2_Hugo_Symbol Site2_Chromosome Site2_Position Site2_Description Site2_Effect_On_Frame NCBI_Build DNA_Support RNA_Support Normal_Read_Count Tumor_Read_Count Normal_Variant_Count Tumor_Variant_Count Normal_Paired_End_Read_Count Tumor_Paired_End_Read_Count Normal_Split_Read_Count Tumor_Split_Read_Count Annotation Breakpoint_Type Center Connection_Type Event_Info Class Length Comments External_Annotation cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation Sv_Status
TCGA-A2-A04P-01 NA KIAA1549 7 138536968 KIAA1549-BRAF.K16B10.COSF509_1 NA BRAF 7 140482957 KIAA1549-BRAF.K16B10.COSF509_2 NA GRCh37 no yes NA 1000 NA 900 NA NA NA NA KIAA1549-BRAF.K16B10.COSF509 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF509 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA NCOA4 10 51582939 NCOA4-RET.N7R12_1 NA RET 10 43612031 NCOA4-RET.N7R12_2 NA GRCh37 no yes NA 1001 NA 800 NA NA NA NA NCOA4-RET.N7R1 NA NA NA Fusion NA NA Gain-of-Function NA NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA EML4 2 42492091 EML4-ALK.E6bA20.AB374362_1 NA ALK 2 29446394 EML4-ALK.E6bA20.AB374362_2 NA GRCh37 no yes NA 1002 NA 700 NA NA NA NA EML4-ALK.E6bA20.AB374362 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB374362 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA TMPRSS2 21 42880007 TMPRSS2-ERG.T1E2.COSF23.1_1 NA ERG 21 39956869 TMPRSS2-ERG.T1E2.COSF23.1_2 NA GRCh37 no yes NA 1003 NA 600 NA NA NA NA TMPRSS2-ERG.T1E2.COSF23.1 NA NA NA Fusion NA NA Gain-of-Function COSMIC:COSF23 NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA EGFR 7 55087058 EGFR-EGFR.E1E8.DelPositive.1_1 NA EGFR 7 55223522 EGFR-EGFR.E1E8.DelPositive.1_2 NA GRCh37 no yes NA 1004 NA 500 NA NA NA NA EGFR-EGFR.E1E8.DelPositive NA NA NA Fusion NA NA NA NA NA NA NA NA SOMATIC
TCGA-A2-A04P-01 NA ALK 2 29497964 ALK-PTPN3.A11P3_1 NA PTPN3 9 112219679 ALK-PTPN3.A11P3_2 NA GRCh37 no yes NA 1005 NA 400 NA NA NA NA ALK-PTPN3.A11P3 NA NA NA Fusion NA NA NA NA NA NA NA NA SOMATIC
TCGA-A1-A0SB-01 NA EML4 2 42522656 EML4-ALK.E13A20.AB462411_1 NA ALK 2 29446335 EML4-ALK.E13A20.AB462411_2 NA GRCh37 no yes NA 1006 NA 300 NA NA NA NA EML4-ALK.E13A20 NA NA NA Fusion NA NA Gain-of-Function GENBANK:AB462411 NA NA NA NA SOMATIC
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