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Fix wave algorithm boundary conditions to prevent invalid alignments #25

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Fix wave algorithm boundary conditions to prevent invalid alignments #25

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8053bfc
Fix wave algorithm boundary conditions to prevent invalid alignments
unavailable-2374 Jan 28, 2026
0001aaf
Add coordinate validation in ALNtoPAF to skip invalid alignments
unavailable-2374 Feb 2, 2026
7d8e0e8
Fix wavefront boundary with dynamic sequence length constraints
unavailable-2374 Feb 4, 2026
e8eda96
fix: Prevent uint8 trace overflow crash in Compress_TraceTo8
unavailable-2374 Feb 17, 2026
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8 changes: 8 additions & 0 deletions ALNtoPAF.c
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Original file line number Diff line number Diff line change
Expand Up @@ -181,6 +181,14 @@ void *gen_paf(void *args)
ascaff = contigs1[acontig].scaf;
bscaff = contigs2[bcontig].scaf;

// Validate alignment coordinates are within bounds
// Skip alignments with invalid coordinates (can occur from edge cases in wave algorithm)
if (path->abpos < 0 || path->aepos > aln->alen || path->abpos >= path->aepos ||
path->bbpos < 0 || path->bepos > aln->blen || path->bbpos >= path->bepos)
{ continue; // Skip this invalid alignment (do NOT set alast, so sequence gets
// reloaded for next valid alignment on this contig)
}

aoff = contigs1[acontig].sbeg;

if (SWAP_G)
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16 changes: 14 additions & 2 deletions FastGA.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3263,7 +3263,17 @@ static void align_contigs(uint8 *beg, uint8 *end, int swide, int ctg1, int ctg2,

rlen = path->aepos - path->abpos;
if (rlen >= alnMin && alnRate*rlen >= path->diffs)
{ Compress_TraceTo8(ovl,0);
{ uint16 *t16 = (uint16 *) ovl->path.trace;
int ti, trace_overflow = 0;
for (ti = 0; ti < ovl->path.tlen; ti++)
if (t16[ti] > 255)
{ trace_overflow = 1;
break;
}
if (trace_overflow)
goto next_alignment;

Compress_TraceTo8(ovl,0);
if (fwrite(ovl,OVL_SIZE,1,tfile) != 1)
{ fprintf(stderr,
"%s: Cannot write overlap gather file %s/%s.%d.las\n",
Expand All @@ -3280,6 +3290,8 @@ static void align_contigs(uint8 *beg, uint8 *end, int swide, int ctg1, int ctg2,
nmem += path->tlen + OVL_SIZE;
}

next_alignment:

#ifdef DEBUG_ALIGN
if (rlen >= ALIGN_MIN && ALIGN_RATE*rlen >= path->diffs)
{ Decompress_TraceTo16(ovl);
Expand Down Expand Up @@ -4933,7 +4945,7 @@ int main(int argc, char *argv[])
gdb2 = gdb1;
else
{ GEXTN2 = ".gdb";
fname = Catenate(PATH1,"/",ROOT1,GEXTN2);
fname = Catenate(PATH2,"/",ROOT2,GEXTN2);
if ((file = fopen(fname,"r")) == NULL)
GEXTN2 = ".1gdb";
else
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