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resure alignment

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This commit is contained in:
Haoyu Cheng
2019-07-12 10:18:25 -04:00
parent 3d88530385
commit f508762557
7 changed files with 1030 additions and 264 deletions
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10
main.cpp
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@@ -138,9 +138,11 @@ void debug_edit_distance()
char* x = "TTCCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGTTCGATTCCATTTCACTCTAGTCCATTCCATTCCATTCAATTCCATTCGACTCTATTCCGTTCCACTCAATTCCATTCCATTCGATTCCATTTTTTTCGAGAACCTTCCATTACACTCCCTTCCATTCCAGTGCATTCCATTCCAGTCTCTTCAGTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCATTCCAGCCCATTCCATTCCATTCCATTCCTTTCCTTTCCGTTTCATTAGATTCCATTGCATTCGATTCCATTCAAATCAATTCCGTTCTATTCAATTTGATTCAT";
char* y = "CCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGTTCGATTCCATTTCACTCTAGTCCATTCCATTCCATTCAATTCCATTCGACTCTATTCCGTTCCATTCAATTCCATTCCATTCGATTCCATTTTTTTCGAGAACCTTCCATTACACTCCCTTCCATTCCAGTGCATTCCATTCCAGTCTCTTCACTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCATTCCAGCCCATTCCATTCCATTCCATTCCTTTCCTTTCCGTTTCATTAGATTCCATTGCATTCCATTCCATTCAATTCAATTCCGTGCTATTCAATTTGATTCATTTCCATTTAATTCCATTCCATTAGATTCCATT";
**/
unsigned short toold = 7;
char* x = "TTCCATACGATTCCATTCAATTCGAGACCATTCTATTCCT";
char* y = "CCATACGATTCCATTCAATTCGAGACCATTCTATTCCTGTCCATTCCTTGTGGT";
unsigned short toold = 15;
char* x
= "GAAAGAGAATCAAATGGAATTGAATCGAATGGAATCGAATGGATTGGAAAGGAATAGAATGGAATGGAATGGAATTGACTCAAATGGAATGGACTAGAATGGAATGGATTCGAATGGAAGGCAAAGGAATGGAATCTATCGGAATGGACTGTAATGGAATGGAATGGAAGGGATTGGAATGGATTCGAATGTAATGGACTGCAATAGAAAGGATTCGAATGGAATGAAAAAGAATTGAATGGAATAGAACAGAATGGAATCAAATCGAAGGAAATGGAATGGAATAGAAAGGAATGGAATGAAATGGAATGGAAAGGATTCGAATGGAATGCAATCGAATGGAATGGAATCGAACGGAATGGAATAAAATGGAAG";
char* y =
"GAAAGAGAATCAAATGGAATTGAATCGAATGGAATCGAATGGATTGGAAAGGAATAGAATGGAATGGAATGGAATGGACTCAAATGGAATGTACTAGAATGGAATGGATTCGAATGGAAGGCAAAGGAATGGAATCTATTGGAATGGACTGTAATGGAATGGAATGGAAGGGATTGGAATGGACTCGAATGGAATGGACTGCAATAGAAAGGATTCGAATGGAATGAAAAAGAATTGAATGGAATAGAACAGAATGGAATCAAATCGAATGAAATGGAATGGAATAGAAAGGAATGGAATGAAATGGAATGGAAAGGATTCGAATGGAATGCAATCGAATGGAATGGAATCGAACGGAATGGAATAAATTTTCTG";
fprintf(stderr, "x_length: %u\n", strlen(x));
fprintf(stderr, "y_length: %u\n", strlen(y));
@@ -204,6 +206,8 @@ int main(int argc, char *argv[])
return 1;
**/
fprintf(stdout, "k-mer length: %d\n",k_mer_length);