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NOT WORKING!!! backup only

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Heng Li
2020-03-24 00:44:56 -04:00
parent e6ef2fb56f
commit 59a9d62df9
8 changed files with 131 additions and 714 deletions
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Trio.cpp
+2 -25
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@@ -8,6 +8,7 @@
#include "Process_Read.h"
#include "Trio.h"
#include "CommandLines.h"
#include "kmer.h"
#define CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr))))
#define MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
@@ -37,30 +38,6 @@ unsigned char seq_nt4_table[256] = { // translate ACGT to 0123
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function
{
key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
key = key ^ key >> 24;
key = ((key + (key << 3)) + (key << 8)) & mask; // key * 265
key = key ^ key >> 14;
key = ((key + (key << 2)) + (key << 4)) & mask; // key * 21
key = key ^ key >> 28;
key = (key + (key << 31)) & mask;
return key;
}
static inline uint64_t yak_hash64_64(uint64_t key)
{
key = ~key + (key << 21);
key = key ^ key >> 24;
key = (key + (key << 3)) + (key << 8);
key = key ^ key >> 14;
key = (key + (key << 2)) + (key << 4);
key = key ^ key >> 28;
key = key + (key << 31);
return key;
}
static inline uint64_t yak_hash_long(uint64_t x[4])
{
int j = x[1] < x[3]? 0 : 1;
@@ -361,4 +338,4 @@ void trio_partition()
fprintf(stderr, "Trio binning has been done.\n");
fprintf(stderr, "%-30s%18.2f\n\n", "Trio binning time:", Get_T() - start_time);
}
}