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Add code for allele counts and BAF stuff. Also update compile scripts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,248 @@ | ||
| /** | ||
| * This class contains the information in a single SNP record | ||
| * @author layla | ||
| * | ||
| */ | ||
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| public class SNPRecord implements Comparable<SNPRecord> | ||
| { | ||
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| //VARIABLES | ||
| public String ID; | ||
| public int chrm; | ||
| public long pos; | ||
| public String strand; | ||
| public String refAllele; | ||
| public String mutAllele; | ||
| public int refCount = 0; | ||
| public int mutCount = 0; | ||
| public int[] allCounts; | ||
| public String otherAlleles; | ||
| public int total; | ||
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| public static String[] ALLELES = {"A","C","G","T"}; | ||
| public static String TAB = "\t"; | ||
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| //CONSTRUCTOR | ||
| public SNPRecord(String anID, int aChrm, long aPos, String aStrand, String aRefAllele, String aMutAllele) | ||
| { | ||
| ID = anID; | ||
| chrm = aChrm; | ||
| pos = aPos; | ||
| strand = aStrand; | ||
| refAllele = aRefAllele; | ||
| mutAllele = aMutAllele; | ||
| refCount = 0; | ||
| mutCount = 0; | ||
| allCounts = new int[4]; | ||
| total = 0; | ||
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| for (int i = 0; i < 4; i++) | ||
| { | ||
| allCounts[i] = 0; | ||
| } | ||
| } | ||
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| //shell constructor | ||
| public SNPRecord(int aChrm, long aPos) | ||
| { | ||
| ID = "temp"; | ||
| chrm = aChrm; | ||
| pos = aPos; | ||
| strand = "+"; | ||
| refAllele = "-"; | ||
| mutAllele = "-"; | ||
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| refCount = 0; | ||
| mutCount = 0; | ||
| allCounts = new int[4]; | ||
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| for (int i = 0; i < 4; i++) | ||
| { | ||
| allCounts[i] = 0; | ||
| } | ||
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| total = 0; | ||
| } | ||
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| //METHODS | ||
| public boolean isContained(int aChrm, long start, long end) | ||
| { | ||
| boolean isContained = false; | ||
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| //Check for correct chrm | ||
| if (aChrm != chrm) | ||
| return isContained; | ||
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| //Interval occurs after SNP | ||
| if (start > pos) | ||
| return isContained; | ||
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| //Interval occurs before SNP | ||
| if (end < pos) | ||
| return isContained; | ||
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| isContained = true; | ||
| return isContained; | ||
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| } | ||
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| public void updateCount(String allele) | ||
| { | ||
| if (allele.equalsIgnoreCase(refAllele)) | ||
| { | ||
| refCount++; | ||
| } | ||
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| if (allele.equalsIgnoreCase(mutAllele)) | ||
| { | ||
| mutCount++; | ||
| } | ||
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| for (int i=0; i < ALLELES.length; i++) | ||
| { | ||
| if (allele.equalsIgnoreCase(ALLELES[i])) | ||
| { | ||
| allCounts[i]=allCounts[i]+1; | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * Returns true if the SNPRecords have the same id, location and strand | ||
| * @return | ||
| */ | ||
| public boolean isSameRecord(SNPRecord aRecord) | ||
| { | ||
| boolean isSame = false; | ||
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| if ((aRecord.ID.equalsIgnoreCase(this.ID)) && | ||
| (aRecord.chrm == this.chrm) && | ||
| (aRecord.pos == this.pos) && | ||
| (aRecord.strand.equalsIgnoreCase(this.strand))) | ||
| isSame = true; | ||
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| return isSame; | ||
| } | ||
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| public void setOtherAlleles(String other) | ||
| { | ||
| otherAlleles = other; | ||
| } | ||
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| public void updateRefAllele(String refAllele, String newStrand) | ||
| { | ||
| String oldStrand = strand; | ||
| this.strand = newStrand; | ||
| this.refAllele = refAllele; | ||
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| String other = this.otherAlleles; | ||
| String[] vals = other.split("/"); | ||
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| if (!oldStrand.equalsIgnoreCase(newStrand)) | ||
| { | ||
| for (int i = 0; i < vals.length; i++) | ||
| { | ||
| if (vals[i].equalsIgnoreCase("A")) | ||
| { | ||
| vals[i] = "T"; | ||
| continue; | ||
| } | ||
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| if (vals[i].equalsIgnoreCase("C")) | ||
| { | ||
| vals[i] = "G"; | ||
| continue; | ||
| } | ||
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| if (vals[i].equalsIgnoreCase("G")) | ||
| { | ||
| vals[i] = "C"; | ||
| continue; | ||
| } | ||
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| if (vals[i].equalsIgnoreCase("T")) | ||
| { | ||
| vals[i] = "A"; | ||
| continue; | ||
| } | ||
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| } | ||
| } | ||
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| if (vals[0].equalsIgnoreCase(refAllele)) | ||
| this.mutAllele = vals[1]; | ||
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| if (vals[1].equalsIgnoreCase(refAllele)) | ||
| this.mutAllele = vals[0]; | ||
| } | ||
|
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| public String toStringForSNPFile() | ||
| { | ||
| StringBuffer sb = new StringBuffer(); | ||
| sb.append(ID); | ||
| sb.append(TAB); | ||
| sb.append(chrm); | ||
| sb.append(TAB); | ||
| sb.append(pos); | ||
| sb.append(TAB); | ||
| sb.append(strand); | ||
| sb.append(TAB); | ||
| sb.append(refAllele); | ||
| sb.append(TAB); | ||
| sb.append(mutAllele); | ||
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| return sb.toString(); | ||
| } | ||
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| public String toStringForCountFile() | ||
| { | ||
| StringBuffer sb = new StringBuffer(); | ||
| sb.append(ID); | ||
| sb.append(TAB); | ||
| sb.append(chrm); | ||
| sb.append(TAB); | ||
| sb.append(pos); | ||
| sb.append(TAB); | ||
| sb.append(strand); | ||
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| for (int i = 0; i < allCounts.length; i++) | ||
| { | ||
| sb.append(TAB); | ||
| sb.append(allCounts[i]); | ||
| } | ||
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| sb.append(TAB); | ||
| sb.append(total); | ||
| sb.append(TAB); | ||
| sb.append(refAllele); | ||
| sb.append(TAB); | ||
| sb.append(refCount); | ||
| sb.append(TAB); | ||
| sb.append(mutAllele); | ||
| sb.append(TAB); | ||
| sb.append(mutCount); | ||
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| return sb.toString(); | ||
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| } | ||
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| @Override | ||
| public int compareTo(SNPRecord other) | ||
| { | ||
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| if (this.chrm < other.chrm) | ||
| return -1; | ||
| else if (this.chrm > other.chrm) | ||
| return 1; | ||
| else if (this.pos < other.pos) | ||
| return -1; | ||
| else if (this.pos > other.pos) | ||
| return 1; | ||
| else | ||
| return 0; | ||
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| } | ||
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| } |
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