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more unused code

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This commit is contained in:
Heng Li
2020-03-26 17:57:39 -04:00
parent 814a3705e2
commit 4aa4ebaf96
7 changed files with 25 additions and 60 deletions
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Assembly.h
-2
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@@ -8,8 +8,6 @@
#define Get_Cigar_Type(RECORD) (RECORD&3)
#define Get_Cigar_Length(RECORD) (RECORD>>2)
void Counting_multiple_thr();
void Build_hash_table_multiple_thr();
void Overlap_calculate_multipe_thr();
void Correct_Reads(int last_round);
#endif
Hash_Table.cpp
-29
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@@ -753,35 +753,6 @@ void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n
}
}
void init_Count_Table(Count_Table** table)
{
*table = ha_ct_init();
}
void init_Pos_Table(Pos_Table** table)
{
*table = ha_pt_init();
}
typedef struct
{
long long* list;
uint64_t length;
} H_peaks;
void insert_H_peaks(H_peaks* h, long long index, long long value)
{
if(h->length <= (uint64_t)index)
{
long long newLen = index + 1;
h->list = (long long*)realloc(h->list, newLen*sizeof(long long));
memset(h->list + h->length, 0, sizeof(long long) * (newLen - h->length));
h->length = newLen;
}
h->list[index] += value;
}
void init_Chain_Data(Chain_Data* x)
{
Hash_Table.h
-4
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@@ -1,12 +1,8 @@
#ifndef __HASHTABLE__
#define __HASHTABLE__
#include "khashl.h"
#include "kmer.h"
#include "htab.h"
KHASHL_MAP_INIT(static inline, Count_Table, ha_ct, uint64_t, int, kh_hash_dummy, kh_eq_generic)
KHASHL_MAP_INIT(static inline, Pos_Table, ha_pt, uint64_t, uint64_t, kh_hash_dummy, kh_eq_generic)
#define PREFIX_BITS 16
#define MAX_SUFFIX_BITS 64
#define MODE_VALUE 101
Makefile
+20 -21
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@@ -32,31 +32,30 @@ depend:
# DO NOT DELETE
Assembly.o: Assembly.h CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h
Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h htab.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h
Assembly.o: Assembly.h CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h
Assembly.o: kmer.h Hash_Table.h htab.h POA.h Correct.h Levenshtein_distance.h
Assembly.o: Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h htab.h
Correct.o: Levenshtein_distance.h POA.h Assembly.h
Hash_Table.o: Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
Hash_Table.o: kvec.h kdq.h CommandLines.h htab.h Correct.h
Hash_Table.o: Levenshtein_distance.h POA.h ksort.h
Correct.o: Correct.h Hash_Table.h kmer.h Process_Read.h Overlaps.h kvec.h
Correct.o: kdq.h CommandLines.h htab.h Levenshtein_distance.h POA.h
Correct.o: Assembly.h
Hash_Table.o: Hash_Table.h kmer.h Process_Read.h Overlaps.h kvec.h kdq.h
Hash_Table.o: CommandLines.h htab.h Correct.h Levenshtein_distance.h POA.h
Hash_Table.o: ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h htab.h Correct.h
Overlaps.o: Levenshtein_distance.h POA.h
POA.o: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h htab.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h CommandLines.h
Overlaps.o: Hash_Table.h kmer.h htab.h Correct.h Levenshtein_distance.h POA.h
POA.o: POA.h Hash_Table.h kmer.h Process_Read.h Overlaps.h kvec.h kdq.h
POA.o: CommandLines.h htab.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
Trio.o: khashl.h kthread.h Process_Read.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h htab.h
hist.o: htab.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
hist.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
htab.o: kthread.h khashl.h kseq.h ksort.h htab.h Process_Read.h Overlaps.h
htab.o: kvec.h kdq.h CommandLines.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h htab.h
sketch.o: kvec.h htab.h Process_Read.h kseq.h Overlaps.h kdq.h CommandLines.h
sys.o: htab.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
main.o: CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h Assembly.h
main.o: Levenshtein_distance.h htab.h
sketch.o: kvec.h htab.h Process_Read.h Overlaps.h kdq.h CommandLines.h
sys.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
Process_Read.h
-3
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@@ -5,7 +5,6 @@
#include <string.h>
#include <stdlib.h>
#include <zlib.h>
#include "kseq.h"
#include "Overlaps.h"
#include "CommandLines.h"
///#include "Hash_Table.h"
@@ -25,7 +24,6 @@
#define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
KSEQ_INIT(gzFile, gzread)
extern uint8_t seq_nt6_table[256];
@@ -39,7 +37,6 @@ extern char rc_Table[5];
#define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
void init_aux_table();
int get_read(kseq_t *s, int adapterLen);
typedef struct
{
Trio.cpp
+4
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@@ -20,6 +20,10 @@
#define YAK_MAGIC "YAK\2"
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#define yak_ch_eq(a, b) ((a)>>YAK_COUNTER_BITS == (b)>>YAK_COUNTER_BITS) // lower 8 bits for counts; higher bits for k-mer
#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)
KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak_ch_eq)
htab.cpp
+1 -1
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@@ -462,7 +462,7 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
* K-mer counting *
******************/
//KSEQ_INIT(gzFile, gzread)
KSEQ_INIT(gzFile, gzread)
#define HAF_COUNT_EXACT 0x1
#define HAF_COUNT_ALL 0x2