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Changed SAMRecord.toString() to emit the SAM format string with all fields #1762

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Changed SAMRecord.toString() to emit the SAM format string with all fields #1762

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26 changes: 2 additions & 24 deletions src/main/java/htsjdk/samtools/SAMRecord.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2368,32 +2368,10 @@ public SAMRecord deepCopy() {
return newSAM;
}

/** Simple toString() that gives a little bit of useful info about the read. */
/** Returns this record formatted as it would appear in a SAM file. */
@Override
public String toString() {
final StringBuilder builder = new StringBuilder(64);
builder.append(getReadName());
if (getReadPairedFlag()) {
if (getFirstOfPairFlag()) {
builder.append(" 1/2");
}
else {
builder.append(" 2/2");
}
}

builder.append(' ')
.append(String.valueOf(getReadLength()))
.append('b');

if (getReadUnmappedFlag()) {
builder.append(" unmapped read.");
}
else {
builder.append(String.format(" aligned to %s:%d-%d.", getContig(), getAlignmentStart(), getAlignmentEnd()));
}

return builder.toString();
return getSAMString();
}

/**
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