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Fix coordinate range check for negative strands in mafNextWithPos #88

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Fix coordinate range check for negative strands in mafNextWithPos #88

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24 changes: 19 additions & 5 deletions src/lib/maf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -192,12 +192,26 @@ for (;;)
textSize, ali->textSize, lf->lineIx, lf->fileName);
}

/* Do some sanity checking. */
/* Do some sanity checking. */
if (comp->srcSize < 0 || comp->size < 0)
errAbort("Got a negative size line %d of %s", lf->lineIx, lf->fileName);
if (comp->start < 0 || comp->start + comp->size > comp->srcSize)
errAbort("Coordinates out of range line %d of %s", lf->lineIx, lf->fileName);

errAbort("Got a negative size line %d of %s", lf->lineIx, lf->fileName);
if (comp->start < 0)
errAbort("Negative start position at line %d of %s", lf->lineIx, lf->fileName);
if (comp->strand == '+')
{
if (comp->start + comp->size > comp->srcSize)
errAbort("Coordinates out of range for positive strand at line %d of %s", lf->lineIx, lf->fileName);
}
else if (comp->strand == '-')
{
if (comp->start > comp->srcSize)
errAbort("Start coordinate out of range for negative strand at line %d of %s", lf->lineIx, lf->fileName);
}
else
{
errAbort("Invalid strand '%c' at line %d of %s", lf->lineIx, lf->fileName);
}

/* Add component to head of list. */
slAddHead(&ali->components, comp);
}
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