more unused code

Assembly.h

@@ -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

@@ -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

@@ -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

@@ -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: Assembly.h CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h
-Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h htab.h POA.h Correct.h
+Assembly.o: kmer.h Hash_Table.h htab.h POA.h Correct.h Levenshtein_distance.h
-Assembly.o: Levenshtein_distance.h Output.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: Correct.h Hash_Table.h kmer.h Process_Read.h Overlaps.h kvec.h
-Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h htab.h
+Correct.o: kdq.h CommandLines.h htab.h Levenshtein_distance.h POA.h
-Correct.o: Levenshtein_distance.h POA.h Assembly.h
+Correct.o: Assembly.h
-Hash_Table.o: Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
+Hash_Table.o: Hash_Table.h kmer.h Process_Read.h Overlaps.h kvec.h kdq.h
-Hash_Table.o: kvec.h kdq.h CommandLines.h htab.h Correct.h
+Hash_Table.o: CommandLines.h htab.h Correct.h Levenshtein_distance.h POA.h
-Hash_Table.o: Levenshtein_distance.h POA.h ksort.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: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h CommandLines.h
-Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h htab.h Correct.h
+Overlaps.o: Hash_Table.h kmer.h htab.h Correct.h Levenshtein_distance.h POA.h
-Overlaps.o: 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: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
+POA.o: CommandLines.h htab.h Correct.h Levenshtein_distance.h
-POA.o: kvec.h kdq.h CommandLines.h htab.h Correct.h Levenshtein_distance.h
+Process_Read.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.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 Overlaps.h kvec.h kdq.h
-Trio.o: khashl.h kthread.h Process_Read.h kseq.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: CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h Assembly.h
-main.o: Assembly.h Levenshtein_distance.h htab.h
+main.o: Levenshtein_distance.h htab.h
-sketch.o: kvec.h htab.h Process_Read.h kseq.h Overlaps.h kdq.h CommandLines.h
+sketch.o: kvec.h htab.h Process_Read.h Overlaps.h kdq.h CommandLines.h
-sys.o: htab.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
+sys.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h

Process_Read.h

@@ -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

@@ -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

@@ -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