shift and scale added to sam output

hasindu2008 · Sep 8, 2023 · 8ccbe93 · 8ccbe93
1 parent d98d5fd
commit 8ccbe93
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Showing 3 changed files with 9 additions and 3 deletions.
diff --git a/src/eventalign.c b/src/eventalign.c
@@ -1878,7 +1878,7 @@ char *emit_event_alignment_sam(char* read_name,
                               bam_hdr_t* base_hdr,
                               bam1_t* base_record,
                               const std::vector<event_alignment_t>& alignments, int8_t sam_out_version,
-                              event_table* et, int64_t len_raw_signal, int64_t ref_len, int8_t rna
+                              event_table* et, int64_t len_raw_signal, int64_t ref_len, int8_t rna, scalings_t scalings
                               )
 {
 
@@ -1958,6 +1958,12 @@ char *emit_event_alignment_sam(char* read_name,
             NEG_CHK(ret_sw);
             ret_sw = bam_aux_append(base_record, "ss", 'Z', strlen(f5c_ss.ss)+1, (uint8_t*)f5c_ss.ss);
             NEG_CHK(ret_sw);
+            float sc = scalings.scale;
+            ret_sw = bam_aux_append(base_record, "sc", 'f', 4, (uint8_t*)(&sc));
+            NEG_CHK(ret_sw);
+            float sh = scalings.shift;
+            ret_sw = bam_aux_append(base_record, "sh", 'f', 4, (uint8_t*)(&sh));
+            NEG_CHK(ret_sw);
             ret_sw = sam_format1(base_hdr, base_record, sp);
             NEG_CHK(ret_sw);
             sprintf_append(sp, "\n");

diff --git a/src/f5c.c b/src/f5c.c
@@ -858,7 +858,7 @@ void eventalign_single(core_t* core, db_t* db, int32_t i){
     } else if(sam_output){
         int8_t sam_out_version = core->opt.sam_out_version;
         int64_t ref_len = core->m_hdr->target_len[db->bam_rec[i]->core.tid];
-        db->event_alignment_result_str[i] = emit_event_alignment_sam(qname, core->m_hdr, db->bam_rec[i], *event_alignment_result, sam_out_version, &(db->et[i]), db->sig[i]->nsample, ref_len, rna);
+        db->event_alignment_result_str[i] = emit_event_alignment_sam(qname, core->m_hdr, db->bam_rec[i], *event_alignment_result, sam_out_version, &(db->et[i]), db->sig[i]->nsample, ref_len, rna, db->scalings[i]);
     } else {
         db->event_alignment_result_str[i] = emit_event_alignment_tsv(0,&(db->et[i]),core->model,core->kmer_size, db->scalings[i],*event_alignment_result, print_read_names, scale_events, write_samples, write_signal_index, collapse_events,
                    db->read_idx[i], qname, contig, db->sig[i]->sample_rate, db->sig[i]->rawptr);

diff --git a/src/f5cmisc.h b/src/f5cmisc.h
@@ -79,7 +79,7 @@ void emit_event_alignment_tsv_header(FILE* fp, int8_t print_read_names, int8_t w
 void emit_sam_header(samFile* fp, const bam_hdr_t* hdr);
 char *emit_event_alignment_sam(char* read_name, bam_hdr_t* base_hdr, bam1_t* base_record,
                               const std::vector<event_alignment_t>& alignments, int8_t sam_out_version,
-                              event_table* et, int64_t len_raw_signal, int64_t ref_len, int8_t rna
+                              event_table* et, int64_t len_raw_signal, int64_t ref_len, int8_t rna, scalings_t scalings
                               );
 void realign_read(std::vector<event_alignment_t>* event_alignment_result, EventalignSummary *summary, FILE *summary_fp,char* ref,
                   const bam_hdr_t* hdr, const bam1_t* record, int32_t read_length,