massive restructure

Makefile

@@ -15,6 +15,10 @@ OBJ = $(BUILD_DIR)/main.o \
 	  $(BUILD_DIR)/misc.o \
 	  $(BUILD_DIR)/sim.o \
 	  $(BUILD_DIR)/thread.o \
+	  $(BUILD_DIR)/format.o \
+	  $(BUILD_DIR)/gensig.o \
+	  $(BUILD_DIR)/genread.o \
+	  $(BUILD_DIR)/ref.o \
 
 PREFIX = /usr/local
 VERSION = `git describe --tags`
@@ -29,7 +33,10 @@ endif
 $(BINARY): $(OBJ) slow5lib/lib/libslow5.a
 	$(CC) $(CFLAGS) $(OBJ) slow5lib/lib/libslow5.a $(LDFLAGS) -o $@
 
-$(BUILD_DIR)/main.o: src/main.c src/misc.h src/error.h  src/sq.h
+HEADERS = src/error.h src/format.h  src/kseq.h  src/misc.h  src/model.h  \
+		 src/prof.h  src/rand.h  src/ref.h  src/seq.h  src/sq.h  src/str.h  src/version.h
+
+$(BUILD_DIR)/main.o: src/main.c $(HEADERS)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
 
 $(BUILD_DIR)/model.o: src/model.c src/model.h  src/misc.h
@@ -38,12 +45,25 @@ $(BUILD_DIR)/model.o: src/model.c src/model.h  src/misc.h
 $(BUILD_DIR)/thread.o: src/thread.c
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
 
-$(BUILD_DIR)/misc.o: src/misc.c
+$(BUILD_DIR)/misc.o: src/misc.c src/error.h
+	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
+
+$(BUILD_DIR)/sim.o: src/sim.c $(HEADERS)
+	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
+
+$(BUILD_DIR)/format.o: src/format.c $(HEADERS)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
 
-$(BUILD_DIR)/sim.o: src/sim.c src/ref.h src/misc.h src/str.h
+$(BUILD_DIR)/gensig.o: src/gensig.c $(HEADERS)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
 
+$(BUILD_DIR)/genread.o: src/genread.c $(HEADERS)
+	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
+
+$(BUILD_DIR)/ref.o: src/ref.c $(HEADERS)
+	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -o $@
+
+
 slow5lib/lib/libslow5.a:
 	$(MAKE) -C slow5lib zstd=$(zstd) no_simd=$(no_simd) zstd_local=$(zstd_local)  lib/libslow5.a
 

src/format.c

@@ -0,0 +1,123 @@
+/* @file  format.c
+** squigulator, a nanopore signal simulator
+**
+** @@
+******************************************************************************/
+/*
+MIT License
+
+Copyright (c) 2023 Hasindu Gamaarachchi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+*/
+
+#include "format.h"
+#include "error.h"
+#include "str.h"
+#include "seq.h"
+#include "version.h"
+
+aln_t *init_aln() {
+    aln_t *aln = (aln_t*)malloc(sizeof(aln_t));
+    MALLOC_CHK(aln);
+    aln->ss_n = 0;
+    aln->ss_c = 1000; //todo can be the readlen
+    aln->ss = (int32_t*)malloc(aln->ss_c * sizeof(int32_t));
+    MALLOC_CHK(aln->ss);
+
+    aln->prefix_end = 0;
+    return aln;
+}
+
+void free_aln(aln_t *aln) {
+    free(aln->ss);
+    free(aln);
+}
+
+char *paf_str(aln_t *aln) {
+    kstring_t str;
+    kstring_t *sp = &str;
+    str_init(sp, aln->tlen*3+1000);
+
+    assert(aln->sig_end > aln->sig_start);
+    sprintf_append(sp, "%s\t%ld\t%ld\t%ld\t%c\t", aln->read_id, (long)aln->len_raw_signal,(long)aln->sig_start, (long)aln->sig_end, aln->strand);
+    //target: name, start, end
+    sprintf_append(sp, "%s\t%ld\t%ld\t%ld\t", aln->tid, aln->tlen, (long)aln->t_st, (long)aln->t_end);
+    //residue matches, block len, mapq
+    int64_t blocklen = aln->t_end - aln->t_st;
+    blocklen = blocklen > 0 ? blocklen : -blocklen;
+    sprintf_append(sp, "%ld\t%ld\t%d\t",blocklen,blocklen,255);
+    sprintf_append(sp, "sc:f:%f\t",1.0);
+    sprintf_append(sp, "sh:f:%f\t",0.0);
+    sprintf_append(sp, "ss:Z:");
+
+    int8_t rna = aln->t_st > aln->t_end ? 1 : 0;
+    for(int i=0; i<aln->ss_n; i++) {
+        int idx = rna ? aln->ss_n - i - 1 : i;
+        sprintf_append(sp, "%d,", aln->ss[idx]);
+    }
+
+    sprintf_append(sp, "\n");
+    str.s[str.l] = '\0';
+    return sp->s;
+}
+
+
+void sam_hdr_wr(FILE *fp, ref_t *ref) {
+    for(int i=0; i<ref->num_ref; i++) {
+        fprintf(fp, "@SQ\tSN:%s\tLN:%ld\n", ref->ref_names[i], (long)ref->ref_lengths[i]);
+    }
+    fprintf(fp, "@PG\tID:squigulator\tPN:squigulator\tVN:%s\n", SQ_VERSION);
+
+}
+
+char *sam_str(aln_t *aln, char *seq, char *rname, int32_t ref_pos_st) {
+    kstring_t str;
+    kstring_t *sp = &str;
+    str_init(sp, aln->tlen*3+1000);
+
+    assert(aln->sig_end > aln->sig_start);
+
+    int flag = aln->strand == '+' ? 0 : 16;
+    sprintf_append(sp, "%s\t%d\t", aln->read_id, flag); //qname, flag
+    sprintf_append(sp, "%s\t%ld\t%d\t", rname, (long)ref_pos_st+1, 255); //rname, pos, mapq
+    sprintf_append(sp, "%ldM\t%c\t%d\t%d\t",strlen(seq), '*', 0, 0); //cigar, rnext, pnext, tlen
+    if (aln->strand == '+'){
+        str_cat(sp, seq, strlen(seq));//seq
+    } else {
+        char *rc = reverse_complement(seq);
+        str_cat(sp, rc, strlen(rc));
+        free(rc);
+    }
+    sprintf_append(sp, "\t%c\t",'*'); //seq, qual
+
+    sprintf_append(sp, "si:Z:%ld,%ld,%ld,%ld\t",(long)aln->sig_start, (long)aln->sig_end, (long)aln->si_st_ref, (long)aln->si_end_ref);
+    sprintf_append(sp, "ss:Z:");
+
+    int8_t rna = aln->t_st > aln->t_end ? 1 : 0;
+    for(int i=0; i<aln->ss_n; i++) {
+        int idx = rna ? aln->ss_n - i - 1 : i;
+        sprintf_append(sp, "%d,", aln->ss[idx]);
+    }
+
+    sprintf_append(sp, "\n");
+    str.s[str.l] = '\0';
+    return sp->s;
+}
+

src/format.h

@@ -0,0 +1,34 @@
+#ifndef SQ_FORMAT_H
+#define SQ_FORMAT_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include "ref.h"
+
+typedef struct {
+    char *read_id;
+    int64_t len_raw_signal;
+    int64_t sig_start;
+    int64_t sig_end;
+    char strand;
+    char *tid;
+    int64_t tlen;
+    int64_t t_st;
+    int64_t t_end;
+
+    int64_t si_st_ref; //for sam
+    int64_t si_end_ref;
+    int32_t *ss;
+    int64_t ss_n;
+    int64_t ss_c;
+
+    int64_t prefix_end;
+} aln_t;
+
+aln_t *init_aln();
+void free_aln(aln_t *aln);
+char *paf_str(aln_t *aln);
+void sam_hdr_wr(FILE *fp, ref_t *ref);
+char *sam_str(aln_t *aln, char *seq, char *rname, int32_t ref_pos_st);
+
+#endif