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canfirtinacanfirtina
committedJun 11, 2023
R10 k-mer models can be parsed now as well.
·
v2.1v1.0
1 parent 12cd032 commit b95f4f2

30 files changed

+94
-204
lines changed
 

‎LICENSE

+3-3
Original file line numberDiff line numberDiff line change
@@ -631,8 +631,8 @@ to attach them to the start of each source file to most effectively
631631
state the exclusion of warranty; and each file should have at least
632632
the "copyright" line and a pointer to where the full notice is found.
633633

634-
Sigmap: a streaming method for mapping nanopore raw signals
635-
Copyright (C) 2020 Haowen Zhang
634+
RawHash: RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
635+
Copyright (C) 2023 Can Firtina
636636

637637
This program is free software: you can redistribute it and/or modify
638638
it under the terms of the GNU General Public License as published by
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
652652
If the program does terminal interaction, make it output a short
653653
notice like this when it starts in an interactive mode:
654654

655-
Sigmap Copyright (C) 2020 Haowen Zhang
655+
RawHash Copyright (C) 2023 Can Firtina
656656
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657657
This is free software, and you are welcome to redistribute it
658658
under certain conditions; type `show c' for details.

‎src/Makefile

+2-2
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ CPPFLAGS=-std=c++11 -Wall -O3 -fopenmp -march=native -DHAVE_KALLOC
1111
# CFLAGS+=-DPROFILERH=1
1212
# CPPFLAGS+=-DPROFILERH=1
1313

14-
OBJS= kthread.o kalloc.o bseq.o roptions.o sequence_until.o rutils.o pore_model.o rsig.o revent.o rsketch.o rawindex.o rmap.o main.o
14+
OBJS= kthread.o kalloc.o bseq.o roptions.o sequence_until.o rutils.o rsig.o revent.o rsketch.o rawindex.o rmap.o main.o
1515

1616
CMAKE_CXX_COMPILER ?= g++
1717
CMAKE_CXX_COMPILER_VERSION ?= $(shell $(CMAKE_CXX_COMPILER) -dumpversion)
@@ -168,4 +168,4 @@ rsig.o: hdf5_tools.hpp kvec.h
168168
rmap.o: rawindex.h rsig.h kthread.h kvec.h rutils.h rsketch.h revent.h sequence_until.h
169169
revent.o: roptions.h kalloc.h
170170
rawindex.o: roptions.h rutils.h rsketch.h rsig.h bseq.h khash.h kvec.h kthread.h
171-
main:o rawhash.h ketopt.h pore_model.h
171+
main:o rawhash.h ketopt.h rutils.h

‎src/main.cpp

+10-11
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@
55

66
#include "rawhash.h"
77
#include "ketopt.h"
8-
#include "pore_model.h" //TODO, remove the CPP dependency
98

109
#define RI_VERSION "0.91"
1110

@@ -47,6 +46,7 @@ static ko_longopt_t long_options[] = {
4746
{ (char*)"test-frequency", ko_required_argument, 320 },
4847
{ (char*)"min-reads", ko_required_argument, 321 },
4948
{ (char*)"sequence-until", ko_no_argument, 322 },
49+
{ (char*)"level_column", ko_required_argument, 323 },
5050
{ 0, 0, 0 }
5151
};
5252

@@ -174,16 +174,20 @@ int main(int argc, char *argv[])
174174
else if (c == 320) opt.ttest_freq = atoi(o.arg);// --test-frequency
175175
else if (c == 321) opt.tmin_reads = atoi(o.arg);// --min-reads
176176
else if (c == 322) opt.flag |= RI_M_SEQUENCEUNTIL;// --sequence-until
177+
else if (c == 323) ipt.lev_col = atoi(o.arg);// --level_column
177178
else if (c == 'V') {puts(RI_VERSION); return 0;}
178179
}
179180

180181
if (argc == o.ind || fp_help == stdout) {
181182
fprintf(fp_help, "Usage: rawhash [options] <target.fa>|<target.idx> [query.fast5] [...]\n");
182183
fprintf(fp_help, "Options:\n");
183-
fprintf(fp_help, " Indexing:\n");
184-
fprintf(fp_help, " -d FILE [Strongly recommended to create before mapping] dump index to FILE [].\n");
184+
fprintf(fp_help, " K-mer (pore) Model:\n");
185185
fprintf(fp_help, " -p FILE pore model FILE [].\n");
186186
fprintf(fp_help, " -k INT size of the k-mers in the pore model [%d]. This is usually 6 for R9.4 and 9 for R10\n", ipt.k);
187+
fprintf(fp_help, " --level_column INT 0-based column index where the mean values are stored in the pore file [%d]. This is usually 1 for both R9.4 and R10\n", ipt.lev_col);
188+
fprintf(fp_help, "\n Indexing:\n");
189+
fprintf(fp_help, " -d FILE [Strongly recommended to create before mapping] dump index to FILE [].\n");
190+
187191
fprintf(fp_help, " -e INT number of events concatanated in a single hash (usually no larger than 10). Also applies during mapping [%d]\n", ipt.e);
188192
fprintf(fp_help, " -q INT most significant bits of signal values to process [%d]. Signal values are assumed to be in the IEEE standard for floating-point arithmetic\n", ipt.q);
189193
fprintf(fp_help, " -l INT least significant bits of the q bits to quantize along with the most signficant 2 bits of the q bits [%d]\n", ipt.lq);
@@ -205,7 +209,7 @@ int main(int argc, char *argv[])
205209
fprintf(fp_help, " --map-best-ratio FLOAT map the read if the ratio between the best and the second-best chain scores is >= FLOAT [%g]\n", opt.min_bestmap_ratio_out);
206210
fprintf(fp_help, " --stop-mean-ratio FLOAT stop chain enlongation if the ratio between the best chain score and the mean chain score is >= FLOAT [%g]\n", opt.min_bestmap_ratio);
207211
fprintf(fp_help, " --map-mean-ratio FLOAT map the read if the ratio between the best chain score and the mean chain score is >= FLOAT [%g]\n", opt.min_meanmap_ratio_out);
208-
fprintf(fp_help, "\n ONT Device:\n");
212+
fprintf(fp_help, "\n Nanopore Parameters:\n");
209213
fprintf(fp_help, " --bp-per-sec INT DNA molecules transiting through the pore (bp per second) [%u]\n", opt.bp_per_sec);
210214
fprintf(fp_help, " --sample-rate INT current sample rate in Hz [%u]\n", opt.sample_rate);
211215
fprintf(fp_help, " --chunk-size INT current samples in a single chunk (by default set to the amount of signals sampled in 1 second) [%u]\n", opt.chunk_size);
@@ -254,17 +258,12 @@ int main(int argc, char *argv[])
254258
ri_idx_reader_close(idx_rdr);
255259
return 1;
256260
}else if(!idx_rdr->is_idx && fpore){
257-
sigmap::PoreModel pore_model;
258-
pore_model.Load(std::string(fpore));
259-
260-
if(pore_model.GetKmerSize() <= 4){
261+
load_pore(fpore, ipt.k, ipt.lev_col, &pore_vals);
262+
if(!pore_vals){
261263
fprintf(stderr, "[ERROR] cannot parse the k-mer pore model file. Please see the example k-mer model files provided in the rawhash repository.\n");
262264
ri_idx_reader_close(idx_rdr);
263265
return 1;
264266
}
265-
pore_vals = (float*)calloc(1U<<(pore_model.GetKmerSize()*2), sizeof(float));
266-
for(uint32_t i = 0; i < 1U<<(pore_model.GetKmerSize()*2); ++i)
267-
pore_vals[i] = pore_model.pore_models_[i].level_mean;
268267
}
269268

270269
while ((ri = ri_idx_reader_read(idx_rdr, pore_vals, n_threads)) != 0) {

‎src/pore_model.cpp

-129
This file was deleted.

‎src/pore_model.h

-35
This file was deleted.

‎src/roptions.c

+1-1
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
void ri_idxopt_init(ri_idxopt_t *opt)
44
{
55
memset(opt, 0, sizeof(ri_idxopt_t));
6-
opt->e = 6; opt->w = 0; opt->q = 9; opt->lq = 3; opt->n = 0; opt->k = 6;
6+
opt->e = 6; opt->w = 0; opt->q = 9; opt->lq = 3; opt->n = 0; opt->k = 6, opt->lev_col = 1;
77
opt->b = 14;
88
opt->mini_batch_size = 50000000;
99
opt->batch_size = 4000000000ULL;

‎src/roptions.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ extern "C" {
1717

1818
// indexing and mapping options
1919
typedef struct ri_idxopt_s{
20-
short b, w, e, n, q, lq, k, flag;
20+
short b, w, e, n, q, lq, k, flag, lev_col;
2121
int64_t mini_batch_size;
2222
uint64_t batch_size;
2323
} ri_idxopt_t;

‎src/rutils.c

+53
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,7 @@
11
#include "rutils.h"
2+
#include <stdlib.h>
3+
#include <string.h>
4+
#include <locale.h>
25
#include <sys/time.h>
36
#include <sys/resource.h>
47

@@ -39,3 +42,53 @@ long ri_peakrss(void)
3942
return r.ru_maxrss;
4043
#endif
4144
}
45+
46+
char* strsep(char** stringp, const char* delim) {
47+
char* start = *stringp;
48+
char* p;
49+
50+
p = (start != NULL) ? strpbrk(start, delim) : NULL;
51+
52+
if (p == NULL) {
53+
*stringp = NULL;
54+
} else {
55+
*p = '\0';
56+
*stringp = p + 1;
57+
}
58+
59+
return start;
60+
}
61+
62+
void load_pore(const char* fpore, const short k, const short lev_col, float** pore_vals){
63+
FILE* fp = fopen(fpore, "r");
64+
if(fp == NULL){
65+
fprintf(stderr, "Error: cannot open file %s\n", fpore);
66+
return;
67+
}
68+
69+
(*pore_vals) = (float*)malloc(sizeof(float) * (1U<<(2*k)));
70+
char line[1024];
71+
char* token;
72+
int i = 0;
73+
while(fgets(line, sizeof(line), fp) != NULL){
74+
if(!strncmp(line, "kmer", 4)) continue;
75+
char* rest = line;
76+
int j = 0;
77+
while((token = strsep(&rest, "\t")) != NULL){
78+
if(j++ == lev_col){
79+
float value;
80+
if (sscanf(token, "%f", &value) == 1) {
81+
(*pore_vals)[i] = value;
82+
} else {
83+
fprintf(stderr, "Error: cannot convert '%s' to float\n", token);
84+
free(pore_vals); pore_vals = NULL;
85+
fclose(fp);
86+
return;
87+
}
88+
break;
89+
}
90+
}
91+
i++;
92+
}
93+
fclose(fp);
94+
}

‎src/rutils.h

+2
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,8 @@ double ri_realtime(void);
2424
double ri_cputime(void);
2525
long ri_peakrss(void);
2626

27+
void load_pore(const char* fpore, const short k, const short lev_col, float** pore_vals);
28+
2729
#ifdef __cplusplus
2830
}
2931
#endif

‎test/evaluation/contamination/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../data/contamination/fast5_files/"
88
REF="../../data/d1_sars-cov-2_r94/ref.fa"
9-
PORE="../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="contamination"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/contamination/run_sigmap.sh

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../data/contamination/fast5_files/"
88
REF="../../data/d1_sars-cov-2_r94/ref.fa"
9-
PORE="../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="contamination"
1111
mkdir -p ${OUTDIR}
1212

@@ -17,7 +17,7 @@ bash ../../scripts/run_sigmap.sh ${OUTDIR} ${PREFIX} ${FAST5} ${REF} ${PORE} ${T
1717
# OUTDIR="./sigmap/"
1818
# FAST5="../../data/d4_human_na12878_r94/fast5_files/"
1919
# REF="../../data/contamination/ref.fa"
20-
# PORE="../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
20+
# PORE="../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
2121
# PREFIX="contamination_neg"
2222
# mkdir -p ${OUTDIR}
2323

‎test/evaluation/read_mapping/d1_sars-cov-2_r94/profile_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ THREAD=$1
88
OUTDIR="./rawhash/"
99
FAST5="../../../data/d1_sars-cov-2_r94/fast5_files/SP1-mapped0.fast5"
1010
REF="../../../data/d1_sars-cov-2_r94/ref.fa"
11-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
11+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1212
PREFIX="d1_sars-cov-2_r94_profile_"${THREAD}
1313
mkdir -p ${OUTDIR}
1414

‎test/evaluation/read_mapping/d1_sars-cov-2_r94/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d1_sars-cov-2_r94/fast5_files/"
88
REF="../../../data/d1_sars-cov-2_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d1_sars-cov-2_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d1_sars-cov-2_r94/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../../data/d1_sars-cov-2_r94/fast5_files/"
88
REF="../../../data/d1_sars-cov-2_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d1_sars-cov-2_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d2_ecoli_r94/profile_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ THREAD=$1
88
OUTDIR="./rawhash/"
99
FAST5="../../../data/d2_ecoli_r94/fast5_files/barcode02_r0barcode02b0_0.fast5"
1010
REF="../../../data/d2_ecoli_r94/ref.fa"
11-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
11+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1212
PREFIX="d2_ecoli_r94_profile_"${THREAD}
1313
mkdir -p ${OUTDIR}
1414

‎test/evaluation/read_mapping/d2_ecoli_r94/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d2_ecoli_r94/fast5_files/"
88
REF="../../../data/d2_ecoli_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d2_ecoli_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d2_ecoli_r94/run_rawhash_pod5.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d2_ecoli_r94/pod5_files/"
88
REF="../../../data/d2_ecoli_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d2_ecoli_r94_pod5"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d2_ecoli_r94/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../../data/d2_ecoli_r94/fast5_files/"
88
REF="../../../data/d2_ecoli_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d2_ecoli_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d3_yeast_r94/profile_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ THREAD=$1
88
OUTDIR="./rawhash/"
99
FAST5="../../../data/d3_yeast_r94/fast5_files/"
1010
REF="../../../data/d3_yeast_r94/ref.fa"
11-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
11+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1212
PREFIX="d3_yeast_r94_profile_"${THREAD}
1313
mkdir -p ${OUTDIR}
1414

‎test/evaluation/read_mapping/d3_yeast_r94/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d3_yeast_r94/fast5_files/"
88
REF="../../../data/d3_yeast_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d3_yeast_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d3_yeast_r94/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../../data/d3_yeast_r94/fast5_files/"
88
REF="../../../data/d3_yeast_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d3_yeast_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d4_green_algae_r94/profile_rawhash.sh

+1-1
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@@ -8,7 +8,7 @@ THREAD=$1
88
OUTDIR="./rawhash/"
99
FAST5="../../../data/d4_green_algae_r94/fast5_files/PCT0062_20180831_0004A30B00232394_1_E5_H5_sequencing_run_PBNP18L0092_0831_A1_29025_read_111_ch_177_strand.fast5"
1010
REF="../../../data/d4_green_algae_r94/ref.fa"
11-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
11+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1212
PREFIX="d4_green_algae_r94_profile_"${THREAD}
1313
mkdir -p ${OUTDIR}
1414

‎test/evaluation/read_mapping/d4_green_algae_r94/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d4_green_algae_r94/fast5_files/"
88
REF="../../../data/d4_green_algae_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d4_green_algae_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d4_green_algae_r94/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../../data/d4_green_algae_r94/fast5_files/"
88
REF="../../../data/d4_green_algae_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d4_green_algae_r94"
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d5_human_na12878_r94/profile_rawhash.sh

+1-1
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@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d5_human_na12878_r94/fast5_files/MinION3_20161013_FNFAB42260_MN20093_sequencing_run_Chip98_Genomic_R9_4_480bps_0.fast5"
88
REF="../../../data/d5_human_na12878_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
1010
PREFIX="d5_human_na12878_r94_profile_"${THREAD}
1111
mkdir -p ${OUTDIR}
1212

‎test/evaluation/read_mapping/d5_human_na12878_r94/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
77
FAST5="../../../data/d5_human_na12878_r94/fast5_files/"
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REF="../../../data/d5_human_na12878_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
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PREFIX="d5_human_na12878_r94"
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mkdir -p ${OUTDIR}
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‎test/evaluation/read_mapping/d5_human_na12878_r94/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./sigmap/"
77
FAST5="../../../data/d5_human_na12878_r94/fast5_files/"
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REF="../../../data/d5_human_na12878_r94/ref.fa"
9-
PORE="../../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
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PREFIX="d5_human_na12878_r94"
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mkdir -p ${OUTDIR}
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‎test/evaluation/relative_abundance/run_rawhash.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
66
OUTDIR="./rawhash/"
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FAST5="../../data/relative_abundance/fast5_files/"
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REF="../../data/relative_abundance/ref.fa"
9-
PORE="../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
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PREFIX="relative_abundance"
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mkdir -p ${OUTDIR}
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‎test/evaluation/relative_abundance/run_sigmap.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ THREAD=$1
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OUTDIR="./sigmap/"
77
FAST5="../../data/relative_abundance/fast5_files/"
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REF="../../data/relative_abundance/ref.fa"
9-
PORE="../../../extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model"
9+
PORE="../../../extern/kmer_models/legacy/legacy_r9.4_180mv_450bps_6mer/template_median68pA.model"
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PREFIX="relative_abundance"
1111
mkdir -p ${OUTDIR}
1212

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