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Logex space consumption issue fixed
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@thegenemyers
thegenemyers committed Oct 23, 2024
1 parent 3b0431c commit ddea6cf
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12 changes: 6 additions & 6 deletions LICENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

· Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
· Redistributions of source code or derivative codes must retain the above
copyright notice, this list of conditions and the following disclaimer.

· Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.
Expand All @@ -27,8 +27,8 @@
For any issues regarding this software and its use, contact EWM at:

Eugene W. Myers Jr.
Bautzner Str. 122e
01099 Dresden
GERMANY
6 Sugar Creek Dr.
Austin, TX 78749
USA
Email: [email protected]

45 changes: 28 additions & 17 deletions Logex.c
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Original file line number Diff line number Diff line change
Expand Up @@ -927,7 +927,7 @@ typedef struct
static int GC[256];
static int GCR[256];

#define IB_OUT 3
static int IB_OUT;

static void gc_setup(int kmer)
{ static int isgc[4] = { 0, 100, 100, 0 };
Expand Down Expand Up @@ -1118,7 +1118,12 @@ static void *merge_thread(void *args)
{ if (DO_TABLE)
{ fwrite(bst+IB_OUT,hbyte,1,out[i]);
fwrite(&one,sizeof(short),1,out[i]);
x = (bst[0] << 16) | (bst[1] << 8) | bst[2];
if (IB_OUT == 3)
x = (bst[0] << 16) | (bst[1] << 8) | bst[2];
else if (IB_OUT == 2)
x = (bst[0] << 8) | bst[1];
else
x = bst[0];
prefx[i][x] += 1;
nels[i] += 1;
}
Expand All @@ -1140,7 +1145,12 @@ static void *merge_thread(void *args)
else
sho = c;
fwrite(&sho,sizeof(short),1,out[i]);
x = (bst[0] << 16) | (bst[1] << 8) | bst[2];
if (IB_OUT == 3)
x = (bst[0] << 16) | (bst[1] << 8) | bst[2];
else if (IB_OUT == 2)
x = (bst[0] << 8) | bst[1];
else
x = bst[0];
prefx[i][x] += 1;
nels[i] += 1;
}
Expand Down Expand Up @@ -1404,9 +1414,21 @@ int main(int argc, char *argv[])
int t, a, i;
int64 p;

for (a = 0; a < narg; a++)
{ range[0][a] = 0;
range[NTHREADS][a] = S[a]->nels;
}

pivot = 0;
for (a = 1; a < narg; a++)
if (S[a]->nels > S[pivot]->nels)
pivot = a;

IB_OUT = S[pivot]->ibyte;
ixlen = (0x1 << (8*IB_OUT));

if (DO_TABLE)
{ ixlen = 0x1000000;
prefx[0] = Malloc(sizeof(int64)*ixlen*nass,"Allocating prefix tables");
{ prefx[0] = Malloc(sizeof(int64)*ixlen*nass,"Allocating prefix tables");
bzero(prefx[0],sizeof(int64)*ixlen*nass);
for (a = 1; a < nass; a++)
prefx[a] = prefx[a-1] + ixlen;
Expand All @@ -1420,16 +1442,6 @@ int main(int argc, char *argv[])
Numbered_Suffix(".ktab.",t+1,"")),"w");
}

for (a = 0; a < narg; a++)
{ range[0][a] = 0;
range[NTHREADS][a] = S[a]->nels;
}

pivot = 0;
for (a = 1; a < narg; a++)
if (S[a]->nels > S[pivot]->nels)
pivot = a;

seq = Current_Kmer(S[0],NULL);
ent = Current_Entry(S[0],NULL);
for (t = 1; t < NTHREADS; t++)
Expand Down Expand Up @@ -1493,7 +1505,6 @@ int main(int argc, char *argv[])

if (DO_TABLE)
{ int minval;
int three = 3;
int mins[narg];

for (a = 0; a < narg; a++)
Expand All @@ -1508,7 +1519,7 @@ int main(int argc, char *argv[])
fwrite(&kmer,sizeof(int),1,f);
fwrite(&NTHREADS,sizeof(int),1,f);
fwrite(&minval,sizeof(int),1,f);
fwrite(&three,sizeof(int),1,f);
fwrite(&IB_OUT,sizeof(int),1,f);

for (i = 1; i < ixlen; i++)
prf[i] += prf[i-1];
Expand Down
23 changes: 19 additions & 4 deletions Profex.c
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
#include "libfastk.h"
#include "ONElib.h"

static char *Usage = "[-1] <source_root>[.prof] [ <read:int>[-(<read:int>|#)] ... ]";
static char *Usage = "[-1z] <source_root>[.prof] [ <read:int>[-(<read:int>|#)] ... ]";

static char *One_Schema =
"P 3 prf This is a 1-code fiel for profiles\n"
Expand All @@ -33,6 +33,7 @@ int main(int argc, char *argv[])
{ Profile_Index *P;
char *command;
int ONE_CODE;
int ZFLAG;

// Process options and capture command line for provenance

Expand Down Expand Up @@ -68,19 +69,21 @@ int main(int argc, char *argv[])
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("1")
ARG_FLAGS("1z")
break;
}
else
argv[j++] = argv[i];
argc = j;

ONE_CODE = flags['1'];
ZFLAG = flags['z'];

if (argc < 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -1: Produce 1-code as output.\n");
fprintf(stderr," -z: Compress runs and ignore zeros.\n");
exit (1);
}
}
Expand Down Expand Up @@ -169,8 +172,20 @@ int main(int argc, char *argv[])
}
else
{ printf("\nRead %d:\n",p);
for (i = 0; i < plen; i++)
printf(" %5d: %5d\n",i,profile[i]);
if (ZFLAG)
{ int last = 0;
for (i = 0; i < plen; i++)
if (profile[i] != last)
{ if (last != 0)
printf(" - %5d (%d)\n",i+P->kmer-1,last);
if (profile[i] != 0)
printf(" %5d",i);
last = profile[i];
}
}
else
for (i = 0; i < plen; i++)
printf(" %5d: %5d\n",i,profile[i]);
}
}
}
Expand Down
7 changes: 7 additions & 0 deletions libfastk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1280,6 +1280,13 @@ inline void GoTo_Kmer_Index(Kmer_Stream *_S, int64 i)

S->cidx = i;

if (i >= S->nels)
{ S->csuf = NULL;
S->cpre = S->ixlen;
S->part = S->nthr+1;
return;
}

p = S->inver[i>>S->shift];
while (index[p] <= i)
p += 1;
Expand Down

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