fix #9461 - mutations api endpoint link fields

core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

@@ -145,11 +145,6 @@ public static int addMutationEvent(ExtendedMutation.MutationEvent event) throws
  event.getTumorSeqAllele(),
  event.getProteinChange(),
  event.getMutationType(),
- event.getFunctionalImpactScore(),
- Float.toString(event.getFisValue()),
- event.getLinkXVar(),
- event.getLinkPdb(),
- event.getLinkMsa(),
  event.getNcbiBuild(),
  event.getStrand(),
  event.getVariantType(),
@@ -800,11 +795,6 @@ private static ExtendedMutation.MutationEvent extractMutationEvent(ResultSet rs)
  event.setEndPosition(rs.getLong("END_POSITION"));
  event.setProteinChange(rs.getString("PROTEIN_CHANGE"));
  event.setMutationType(rs.getString("MUTATION_TYPE"));
- event.setFunctionalImpactScore(rs.getString("FUNCTIONAL_IMPACT_SCORE"));
- event.setFisValue(rs.getFloat("FIS_VALUE"));
- event.setLinkXVar(rs.getString("LINK_XVAR"));
- event.setLinkPdb(rs.getString("LINK_PDB"));
- event.setLinkMsa(rs.getString("LINK_MSA"));
  event.setNcbiBuild(rs.getString("NCBI_BUILD"));
  event.setStrand(rs.getString("STRAND"));
  event.setVariantType(rs.getString("VARIANT_TYPE"));

core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java

@@ -44,6 +44,7 @@
  */
 public final class ExtendedMutation
 {
+
  public final static class MutationEvent {
  private long mutationEventId;
  private CanonicalGene gene;
@@ -52,12 +53,7 @@ public final static class MutationEvent {
  private long endPosition;
  private String proteinChange; // amino acid change
  private String mutationType; // variant classification
- private String functionalImpactScore;
- private float fisValue;
- private String linkXVar;
- private String linkPdb;
- private String linkMsa;
- private String keyword;
+ private String keyword;
  private String ncbiBuild;
  private String strand;
  private String variantType;
@@ -132,46 +128,6 @@ public void setMutationType(String mutationType) {
  this.mutationType = mutationType;
  }
 
- public String getFunctionalImpactScore() {
- return functionalImpactScore;
- }
-
- public void setFunctionalImpactScore(String functionalImpactScore) {
- this.functionalImpactScore = functionalImpactScore;
- }
-
- public float getFisValue() {
- return fisValue;
- }
-
- public void setFisValue(float fisValue) {
- this.fisValue = fisValue;
- }
-
- public String getLinkXVar() {
- return linkXVar;
- }
-
- public void setLinkXVar(String linkXVar) {
- this.linkXVar = linkXVar;
- }
-
- public String getLinkPdb() {
- return linkPdb;
- }
-
- public void setLinkPdb(String linkPdb) {
- this.linkPdb = linkPdb;
- }
-
- public String getLinkMsa() {
- return linkMsa;
- }
-
- public void setLinkMsa(String linkMsa) {
- this.linkMsa = linkMsa;
- }
-
  public String getKeyword() {
  return keyword;
  }
@@ -543,47 +499,7 @@ public void setAminoAcidChange(String aminoAcidChange)
  {
  this.aminoAcidChange = aminoAcidChange;
  }
-
- public String getFunctionalImpactScore() {
- return event.getFunctionalImpactScore();
- }
-
- public void setFunctionalImpactScore(String fImpact) {
- event.setFunctionalImpactScore(fImpact);
- }
-
- public float getFisValue() {
- return event.getFisValue();
- }
-
- public void setFisValue(Float fisValue) {
- event.setFisValue(fisValue);
- }
-
- public String getLinkXVar() {
- return event.getLinkXVar();
- }
-
- public void setLinkXVar(String linkXVar) {
- event.setLinkXVar(linkXVar);
- }
-
- public String getLinkPdb() {
- return event.getLinkPdb();
- }
-
- public void setLinkPdb(String linkPdb) {
- event.setLinkPdb(linkPdb);
- }
-
- public String getLinkMsa() {
- return event.getLinkMsa();
- }
-
- public void setLinkMsa(String linkMsa) {
- event.setLinkMsa(linkMsa);
- }
-
+
  public String getSequencer() {
  return sequencer;
  }
@@ -837,7 +753,7 @@ public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId)
  {
  event.setOncotatorRefseqMrnaId(oncotatorRefseqMrnaId);
  }
-
+ 
  public String getOncotatorUniprotName()
  {
  return event.getOncotatorUniprotName();

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java

@@ -206,31 +206,6 @@ public void importData() throws IOException, DaoException {
  if (record.getEndPosition() < 0)
  record.setEndPosition(0);
 
- String functionalImpactScore = "";
- // using -1 is not safe, FIS can be a negative value
- Float fisValue = Float.MIN_VALUE;
- String linkXVar = "";
- String linkMsa = "";
- String linkPdb = "";
-
- if (fileHasOMAData)
- {
-// functionalImpactScore = getField(parts, "MA:FImpact" );
-// fisValue = getField(parts, "MA:FIS");
-// linkXVar = getField(parts, "MA:link.var" );
-// linkMsa = getField(parts, "MA:link.MSA" );
-// linkPdb = getField(parts, "MA:link.PDB" );
-
- functionalImpactScore = record.getMaFuncImpact();
- fisValue = record.getMaFIS();
- linkXVar = record.getMaLinkVar();
- linkMsa = record.getMaLinkMsa();
- linkPdb = record.getMaLinkPdb();
-
- functionalImpactScore = transformOMAScore(functionalImpactScore);
- linkXVar = linkXVar.replace("\"", "");
- }
-
  String mutationType,
  proteinChange,
  aaChange,
@@ -361,11 +336,6 @@ public void importData() throws IOException, DaoException {
  mutation.setEndPosition(record.getEndPosition());
  mutation.setValidationStatus(record.getValidationStatus());
  mutation.setMutationStatus(record.getMutationStatus());
- mutation.setFunctionalImpactScore(functionalImpactScore);
- mutation.setFisValue(fisValue);
- mutation.setLinkXVar(linkXVar);
- mutation.setLinkPdb(linkPdb);
- mutation.setLinkMsa(linkMsa);
  mutation.setNcbiBuild(record.getNcbiBuild());
  mutation.setStrand(record.getStrand());
  mutation.setVariantType(record.getVariantType());

core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java

@@ -298,11 +298,6 @@ public static ExtendedMutation newMutation() {
  mutation.setEndPosition(defaultLong);
  mutation.setValidationStatus(defaultStr);
  mutation.setMutationStatus(defaultStr);
- mutation.setFunctionalImpactScore(defaultStr);
- mutation.setFisValue(defaultFloat);
- mutation.setLinkXVar(defaultStr);
- mutation.setLinkPdb(defaultStr);
- mutation.setLinkMsa(defaultStr);
  mutation.setNcbiBuild(defaultStr);
  mutation.setStrand(defaultStr);
  mutation.setVariantType(defaultStr);

core/src/main/java/org/mskcc/cbio/portal/web_api/GetMutationData.java

@@ -182,10 +182,6 @@ public static String getProfileData(String geneticProfileId,
  buf.append(mutation.getMutationType()).append(TAB);
  buf.append(mutation.getValidationStatus()).append(TAB);
  buf.append(mutation.getProteinChange()).append(TAB);
- buf.append(mutation.getFunctionalImpactScore()).append(TAB);
- buf.append(mutation.getLinkXVar()).append(TAB);
- buf.append(mutation.getLinkPdb()).append(TAB);
- buf.append(mutation.getLinkMsa()).append(TAB);
  buf.append(mutation.getChr()).append(TAB);
  buf.append(mutation.getStartPosition()).append(TAB);
  buf.append(mutation.getEndPosition()).append(TAB);

core/src/test/java/org/mskcc/cbio/portal/dao/TestDaoMutation.java

@@ -101,11 +101,6 @@ private void runTheTest() throws DaoException{
  mutation.setSequencingCenter("Broad");
  mutation.setSequencer("SOLiD");
  mutation.setProteinChange("BRCA1_123");
- mutation.setFunctionalImpactScore("H");
- mutation.setFisValue(Float.MIN_VALUE);
- mutation.setLinkXVar("link1");
- mutation.setLinkPdb("link2");
- mutation.setLinkMsa("link3");
  mutation.setNcbiBuild("37/hg19");
  mutation.setStrand("+");
  mutation.setVariantType("Consolidated");
@@ -174,11 +169,6 @@ private void validateMutation(ExtendedMutation mutation) {
  assertEquals("Broad", mutation.getSequencingCenter());
  assertEquals("SOLiD", mutation.getSequencer());
  assertEquals("BRCA1_123", mutation.getProteinChange());
- assertEquals("H", mutation.getFunctionalImpactScore());
- assertEquals(Float.MIN_VALUE, mutation.getFisValue(), 1E-30);
- assertEquals("link1", mutation.getLinkXVar());
- assertEquals("link2", mutation.getLinkPdb());
- assertEquals("link3", mutation.getLinkMsa());
  assertEquals("37/hg19", mutation.getNcbiBuild());
  assertEquals("+", mutation.getStrand());
  assertEquals("Consolidated", mutation.getVariantType());

core/src/test/resources/seed_mini.sql

@@ -411,9 +411,9 @@ INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALU
 INSERT INTO "sample" ("INTERNAL_ID","STABLE_ID","SAMPLE_TYPE","PATIENT_ID") VALUES (19,'TCGA-A1-A0SB-02','Primary Solid Tumor',1);
 
 -- mutation_event
-INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','NA',0,'getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all','NA','NA','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating');
-INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','H',4.355,'getma.org/?cm=var&var=hg19,17,41258504,A,C&fts=all','getma.org/pdb.php?prot=BRCA1_HUMAN&from=24&to=64&var=C61G','getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=24&re=64&var=C61G','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense');
-INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","FUNCTIONAL_IMPACT_SCORE","FIS_VALUE","LINK_XVAR","LINK_PDB","LINK_MSA","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','NA',1.4013e-45,'NA','NA','NA','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating');
+INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2038,672,'17',41244748,41244748,'G','A','Q934*','Nonsense_Mutation','37','+','SNP','rs80357223','unknown','rs80357223','NM_007294','c.(2800-2802)CAG>TAG','BRCA1_HUMAN','P38398',934,934,1,'BRCA1 truncating');
+INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (22604,672,'17',41258504,41258504,'A','C','C61G','Missense_Mutation','37','+','SNP','rs28897672','byCluster','rs28897672','NM_007294','c.(181-183)TGT>GGT','BRCA1_HUMAN','P38398',61,61,1,'BRCA1 C61 missense');
+INSERT INTO "mutation_event" ("MUTATION_EVENT_ID","ENTREZ_GENE_ID","CHR","START_POSITION","END_POSITION","REFERENCE_ALLELE","TUMOR_SEQ_ALLELE","PROTEIN_CHANGE","MUTATION_TYPE","NCBI_BUILD","STRAND","VARIANT_TYPE","DB_SNP_RS","DB_SNP_VAL_STATUS","ONCOTATOR_DBSNP_RS","ONCOTATOR_REFSEQ_MRNA_ID","ONCOTATOR_CODON_CHANGE","ONCOTATOR_UNIPROT_ENTRY_NAME","ONCOTATOR_UNIPROT_ACCESSION","ONCOTATOR_PROTEIN_POS_START","ONCOTATOR_PROTEIN_POS_END","CANONICAL_TRANSCRIPT","KEYWORD") VALUES (2039,672,'17',41276033,41276033,'C','T','C27_splice','Splice_Site','37','+','SNP','rs80358010','byCluster','rs80358010','NM_007294','c.e2+1','NA','NA',-1,-1,1,'BRCA1 truncating');
 
 -- mutation
 INSERT INTO "mutation" ("MUTATION_EVENT_ID","GENETIC_PROFILE_ID","SAMPLE_ID","ENTREZ_GENE_ID","CENTER","SEQUENCER","MUTATION_STATUS","VALIDATION_STATUS","TUMOR_SEQ_ALLELE1","TUMOR_SEQ_ALLELE2","MATCHED_NORM_SAMPLE_BARCODE","MATCH_NORM_SEQ_ALLELE1","MATCH_NORM_SEQ_ALLELE2","TUMOR_VALIDATION_ALLELE1","TUMOR_VALIDATION_ALLELE2","MATCH_NORM_VALIDATION_ALLELE1","MATCH_NORM_VALIDATION_ALLELE2","VERIFICATION_STATUS","SEQUENCING_PHASE","SEQUENCE_SOURCE","VALIDATION_METHOD","SCORE","BAM_FILE","TUMOR_ALT_COUNT","TUMOR_REF_COUNT","NORMAL_ALT_COUNT","NORMAL_REF_COUNT") VALUES (2038,6,6,672,'genome.wustl.edu','IlluminaGAIIx','Germline','Unknown','G','A','TCGA-A1-A0SH-10A-03D-A099-09','G','A','NA','NA','NA','NA','Unknown','Phase_IV','Capture','NA','1','dbGAP',-1,-1,-1,-1);

db-scripts/src/main/resources/cgds.sql

@@ -435,11 +435,6 @@ CREATE TABLE `mutation_event` (
  `TUMOR_SEQ_ALLELE` text,
  `PROTEIN_CHANGE` varchar(255),
  `MUTATION_TYPE` varchar(255) COMMENT 'e.g. Missense, Nonsence, etc.',
- `FUNCTIONAL_IMPACT_SCORE` varchar(50) COMMENT 'Result from OMA/XVAR.',
- `FIS_VALUE` float,
- `LINK_XVAR` varchar(500) COMMENT 'Link to OMA/XVAR Landing Page for the specific mutation.',
- `LINK_PDB` varchar(500),
- `LINK_MSA` varchar(500),
  `NCBI_BUILD` varchar(10),
  `STRAND` varchar(2),
  `VARIANT_TYPE` varchar(15),

db-scripts/src/main/resources/migration.sql

@@ -978,6 +978,8 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.12";
 ALTER TABLE `sample` MODIFY COLUMN `STABLE_ID` VARCHAR(63) NOT NULL;
 UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13";
 
+
+
 ##version: 2.12.14
 ALTER TABLE `structural_variant` MODIFY COLUMN `SITE1_ENTREZ_GENE_ID` int(11);
 ALTER TABLE `structural_variant` ADD COLUMN `SITE1_REGION` varchar(25) AFTER `SITE1_CHROMOSOME`;
@@ -992,3 +994,12 @@ ALTER TABLE `structural_variant` DROP COLUMN `SITE2_EXON`;
 ALTER TABLE `structural_variant` DROP COLUMN `CENTER`;
 ALTER TABLE `structural_variant` DROP COLUMN `EXTERNAL_ANNOTATION`;
 UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14";
+
+
+-- changes for issue 9461
+ALTER TABLE `mutation_event` DROP COLUMN `FUNCTIONAL_IMPACT_SCORE`;
+ALTER TABLE `mutation_event` DROP COLUMN `FIS_VALUE`;
+ALTER TABLE `mutation_event` DROP COLUMN `LINK_XVAR`;
+ALTER TABLE `mutation_event` DROP COLUMN `LINK_PDB`;
+ALTER TABLE `mutation_event` DROP COLUMN `LINK_MSA`;
+UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14";

model/src/main/java/org/cbioportal/model/Mutation.java

@@ -23,11 +23,6 @@ public class Mutation extends Alteration implements Serializable {
  private String tumorSeqAllele;
  private String proteinChange;
  private String mutationType;
- private String functionalImpactScore;
- private BigDecimal fisValue;
- private String linkXvar;
- private String linkPdb;
- private String linkMsa;
  private String ncbiBuild;
  private String variantType;
  private String oncotatorRefseqMrnaId;
@@ -155,46 +150,6 @@ public void setMutationType(String mutationType) {
  this.mutationType = mutationType;
  }
 
- public String getFunctionalImpactScore() {
- return functionalImpactScore;
- }
-
- public void setFunctionalImpactScore(String functionalImpactScore) {
- this.functionalImpactScore = functionalImpactScore;
- }
-
- public BigDecimal getFisValue() {
- return fisValue;
- }
-
- public void setFisValue(BigDecimal fisValue) {
- this.fisValue = fisValue;
- }
-
- public String getLinkXvar() {
- return linkXvar;
- }
-
- public void setLinkXvar(String linkXvar) {
- this.linkXvar = linkXvar;
- }
-
- public String getLinkPdb() {
- return linkPdb;
- }
-
- public void setLinkPdb(String linkPdb) {
- this.linkPdb = linkPdb;
- }
-
- public String getLinkMsa() {
- return linkMsa;
- }
-
- public void setLinkMsa(String linkMsa) {
- this.linkMsa = linkMsa;
- }
-
  public String getNcbiBuild() {
  return ncbiBuild;
  }
@@ -210,15 +165,14 @@ public String getVariantType() {
  public void setVariantType(String variantType) {
  this.variantType = variantType;
  }
-
  public String getOncotatorRefseqMrnaId() {
  return oncotatorRefseqMrnaId;
  }
 
  public void setOncotatorRefseqMrnaId(String oncotatorRefseqMrnaId) {
  this.oncotatorRefseqMrnaId = oncotatorRefseqMrnaId;
  }
-
+ 
  public Integer getOncotatorProteinPosStart() {
  return oncotatorProteinPosStart;
  }

persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml

@@ -26,11 +26,6 @@
  mutation_event.TUMOR_SEQ_ALLELE AS tumorSeqAllele,
  mutation_event.PROTEIN_CHANGE AS proteinChange,
  mutation_event.MUTATION_TYPE AS mutationType,
- mutation_event.FUNCTIONAL_IMPACT_SCORE AS functionalImpactScore,
- mutation_event.FIS_VALUE AS fisValue,
- mutation_event.LINK_XVAR AS linkXvar,
- mutation_event.LINK_PDB AS linkPdb,
- mutation_event.LINK_MSA AS linkMsa,
  mutation_event.NCBI_BUILD AS ncbiBuild,
  mutation_event.VARIANT_TYPE AS variantType,
  mutation_event.ONCOTATOR_REFSEQ_MRNA_ID AS oncotatorRefseqMrnaId,

persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java

@@ -192,11 +192,6 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr
  Assert.assertEquals("BRCA1 truncating", mutation.getKeyword());
  Assert.assertEquals("Germline", mutation.getMutationStatus());
  Assert.assertEquals("Nonsense_Mutation", mutation.getMutationType());
- Assert.assertEquals("NA", mutation.getFunctionalImpactScore());
- Assert.assertEquals(new BigDecimal("0.0"), mutation.getFisValue());
- Assert.assertEquals("getma.org/?cm=var&var=hg19,17,41244748,G,A&fts=all", mutation.getLinkXvar());
- Assert.assertEquals("NA", mutation.getLinkPdb());
- Assert.assertEquals("NA", mutation.getLinkMsa());
  Assert.assertEquals("37", mutation.getNcbiBuild());
  Assert.assertEquals((Integer) (-1), mutation.getNormalAltCount());
  Assert.assertEquals((Integer) (-1), mutation.getNormalRefCount());