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Following changes to get rid of Canonicalization #38

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Following changes to get rid of Canonicalization #38

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17 changes: 2 additions & 15 deletions src/count.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,6 @@ bool reads_to_kmers(chunk &c, flush_object *obj)
goto next_read;
{
__int128_t first = 0;
__int128_t first_rev = 0;
__int128_t item = 0;
for(uint32_t i = 0; i < obj->ksize; i++) { //First kmer
uint8_t curr = Kmer::map_base(read[i]);
Expand All @@ -111,12 +110,8 @@ bool reads_to_kmers(chunk &c, flush_object *obj)
first = first << 2;
}
first = first >> 2;
first_rev = Kmer::reverse_complement(first, obj->ksize);

if (Kmer::compare_kmers(first, first_rev))
item = first;
else
item = first_rev;
item = first;

/*
* first try and insert in the main QF.
Expand All @@ -140,7 +135,6 @@ bool reads_to_kmers(chunk &c, flush_object *obj)
}

uint64_t next = (first << 2) & BITMASK(2 * obj->ksize);
uint64_t next_rev = first_rev >> 2;

for(uint32_t i = obj->ksize; i < read.length(); i++) { //next kmers
uint8_t curr = Kmer::map_base(read[i]);
Expand All @@ -152,13 +146,7 @@ bool reads_to_kmers(chunk &c, flush_object *obj)
goto start_read;
}
next |= curr;
uint64_t tmp = Kmer::reverse_complement_base(curr);
tmp <<= (obj->ksize * 2 - 2);
next_rev = next_rev | tmp;
if (Kmer::compare_kmers(next, next_rev))
item = next;
else
item = next_rev;
item = next;

/*
* first try and insert in the main QF.
Expand All @@ -182,7 +170,6 @@ bool reads_to_kmers(chunk &c, flush_object *obj)
}

next = (next << 2) & BITMASK(2*obj->ksize);
next_rev = next_rev >> 2;
}
}

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