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update polishing

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chhylp123
2020-10-19 13:22:45 -04:00
parent 9d4e3b3283
commit e5d503ea65
2 changed files with 178 additions and 216 deletions
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sketch.cpp
+3 -1
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@@ -183,10 +183,12 @@ kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct)
}
tq_push(&tq, skip_len);
kmer_span += skip_len;
///how many bases that are covered by this HPC k-mer
///kmer_span includes at most k HPC elements
if (tq.count > k) kmer_span -= tq_shift(&tq);
} else kmer_span = l + 1 < k? l + 1 : k;
///kmer_span should be used for HPC k-mer
///so for non-HPC k-mer, kmer_span should be k in any case?
///non-HPC k-mer, kmer_span should be k
///kmer_span is used to calculate anchor pos on reverse complementary strand
if(k_flag != NULL) k_flag->a.a[i] = 1;///lable all useful base, which are not ignored by HPC