@Override public boolean equals(final Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; final SAMFileHeader that = (SAMFileHeader) o; if (!attributesEqual(that)) return false; if (mProgramRecords != null ? !mProgramRecords.equals(that.mProgramRecords) : that.mProgramRecords != null) return false; if (mReadGroups != null ? !mReadGroups.equals(that.mReadGroups) : that.mReadGroups != null) return false; if (mSequenceDictionary != null ? !mSequenceDictionary.equals(that.mSequenceDictionary) : that.mSequenceDictionary != null) return false; return true; }
@Override public boolean equals(final Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; final SAMFileHeader that = (SAMFileHeader) o; if (!attributesEqual(that)) return false; if (mProgramRecords != null ? !mProgramRecords.equals(that.mProgramRecords) : that.mProgramRecords != null) return false; if (mReadGroups != null ? !mReadGroups.equals(that.mReadGroups) : that.mReadGroups != null) return false; if (mSequenceDictionary != null ? !mSequenceDictionary.equals(that.mSequenceDictionary) : that.mSequenceDictionary != null) return false; return true; }
@Override public boolean equals(final Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; final SAMFileHeader that = (SAMFileHeader) o; if (!attributesEqual(that)) return false; if (mProgramRecords != null ? !mProgramRecords.equals(that.mProgramRecords) : that.mProgramRecords != null) return false; if (mReadGroups != null ? !mReadGroups.equals(that.mReadGroups) : that.mReadGroups != null) return false; if (mSequenceDictionary != null ? !mSequenceDictionary.equals(that.mSequenceDictionary) : that.mSequenceDictionary != null) return false; return true; }
if (!normalHeader.getSequenceDictionary().equals(tumorHeader.getSequenceDictionary())) { Logger.error("Reference Sequences for tumor and normal do not match. Check the VCF headers.");
} else if (dict.equals(in.getFileHeader().getSequenceDictionary())) { in.getFileHeader().setSequenceDictionary(dict);
} else if (dict.equals(in.getFileHeader().getSequenceDictionary())) { in.getFileHeader().setSequenceDictionary(dict);