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Remove redundant and unused BAM_FLAGS from CRAM code. #1292

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Feb 20, 2019
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Remove redundant and unused BAM_FLAGS from CRAM code. #1292

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21 changes: 0 additions & 21 deletions src/main/java/htsjdk/samtools/cram/structure/CramCompressionRecord.java
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Original file line number Diff line number Diff line change
Expand Up @@ -345,25 +345,4 @@ public void setSupplementary(final boolean supplementary) {
flags = supplementary ? flags | SUPPLEMENTARY_FLAG : flags & ~SUPPLEMENTARY_FLAG;
}

public static class BAM_FLAGS {
public static final int READ_PAIRED_FLAG = 0x1;
public static final int PROPER_PAIR_FLAG = 0x2;
public static final int READ_UNMAPPED_FLAG = 0x4;
public static final int MATE_UNMAPPED_FLAG = 0x8;
public static final int READ_STRAND_FLAG = 0x10;
public static final int MATE_STRAND_FLAG = 0x20;
public static final int FIRST_OF_PAIR_FLAG = 0x40;
public static final int SECOND_OF_PAIR_FLAG = 0x80;
public static final int NOT_PRIMARY_ALIGNMENT_FLAG = 0x100;
public static final int READ_FAILS_VENDOR_QUALITY_CHECK_FLAG = 0x200;
public static final int DUPLICATE_READ_FLAG = 0x400;
public static final int SUPPLEMENTARY_FLAG = 0x800;
}

public static int getBAMFlags(final int cramFlags, final byte cramMateFlags) {
int value = cramFlags;
if ((cramMateFlags & MATE_NEG_STRAND_FLAG) != 0) value |= BAM_FLAGS.MATE_STRAND_FLAG;
if ((cramMateFlags & MATE_UNMAPPED_FLAG) != 0) value |= BAM_FLAGS.MATE_UNMAPPED_FLAG;
return value;
}
}