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Add reverse lexicographical order #28

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Add reverse lexicographical order #28

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30 changes: 30 additions & 0 deletions src/fastq-sort.c
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Original file line number Diff line number Diff line change
Expand Up @@ -334,6 +334,30 @@ int seq_cmp_seq(const void* a, const void* b)
return strcmp(((seq_t*) a)->seq.s, ((seq_t*) b)->seq.s);
}

int seq_cmp_rlo(const void* a, const void* b)
{
//read right-to-left
size_t offset_a=((seq_t*) a)->seq.n - 1;
size_t offset_b=((seq_t*) b)->seq.n - 1;

while( *((((seq_t*) a)->seq.s)+offset_a)==*((((seq_t*) b)->seq.s)+offset_b) && offset_a>=0 && offset_b>=0){
offset_a--;
offset_b--;
}

if(offset_a>=0 && offset_b>=0){
if(*((((seq_t*) a)->seq.s)+offset_a)<*((((seq_t*) b)->seq.s)+offset_b))
return -1;
else
return 1;
}
else if(offset_a<0 && offset_b>=0)
return -1;
else if(offset_a>=0 && offset_b<0)
return 1;
else
return 0;
}

static float seq_gc(const seq_t* s)
{
Expand Down Expand Up @@ -446,6 +470,7 @@ void print_help()
" -i, --id sort alphabetically by read identifier\n"
" -n, --idn sort alphanumerically by read identifier according to \"samtools sort -n\"\n"
" -s, --seq sort alphabetically by sequence\n"
" -c, --rlo sort co-lexicographically (i.e., reverse lexicographical order) by sequence\n"
" -R, --random randomly shuffle the sequences\n"
" --seed[=SEED] seed to use for random shuffle.\n"
" -G, --gc sort by GC content\n"
Expand Down Expand Up @@ -491,6 +516,7 @@ int main(int argc, char* argv[])
{"id", no_argument, NULL, 'i'},
{"idn", no_argument, NULL, 'n'},
{"seq", no_argument, NULL, 's'},
{"rlo", no_argument, NULL, 'c'},
{"random", no_argument, NULL, 'R'},
{"seed", optional_argument, NULL, 0},
{"gc", no_argument, NULL, 'G'},
Expand Down Expand Up @@ -528,6 +554,10 @@ int main(int argc, char* argv[])
case 's':
user_cmp = seq_cmp_seq;
break;

case 'c':
user_cmp = seq_cmp_rlo;
break;

case 'R':
user_cmp = seq_cmp_hash;
Expand Down