diff --git a/src/main-functions/find_isoform.cpp b/src/main-functions/find_isoform.cpp
new file mode 100755
index 0000000..4ec163c
--- /dev/null
+++ b/src/main-functions/find_isoform.cpp
@@ -0,0 +1,79 @@
+#include "find_isoform.h"
+
+#include <string>
+#include <unordered_map>
+#include <vector>
+#include <utility>
+
+#include "../classes/GFFData.h"
+#include "../classes/GeneAnnotationParser.h"
+#include "../classes/junctions.h"
+#include "../classes/Pos.h"
+#include "get_transcript_seq.h"
+#include "group_bam2isoform.h"
+
+void
+find_isoform
+(
+    const std::string &gff3,
+    const std::string &genome_bam,
+    const std::string &isoform_gff3,
+    const std::string &tss_tes_stat,
+    const std::string &genomefa,
+    const std::string &transcript_fa,
+    const Rcpp::List  &isoform_parameters,
+    const std::string &raw_splice_isoform)
+{
+    Rcpp::Rcout << "#### Reading Gene Annotations\n";
+
+    GFFData gene_annotation = parse_gff_file(gff3);
+
+    std::unordered_map<std::string, Junctions>
+    transcript_to_junctions = map_transcripts_to_junctions(
+        gene_annotation.transcript_to_exon
+    );
+
+    gene_annotation.gene_to_transcript = remove_similar_tr(
+        gene_annotation.gene_to_transcript,
+        gene_annotation.transcript_to_exon,
+        10
+    );
+
+    std::unordered_map<std::string, std::vector<exon>>
+    gene_dict = get_gene_flat(
+        gene_annotation.gene_to_transcript,
+        gene_annotation.transcript_to_exon
+    );
+
+    std::unordered_map<std::string, std::vector<GeneBlocks>>
+    chr_to_blocks = get_gene_blocks(
+        gene_dict, 
+        gene_annotation.chr_to_gene,
+        gene_annotation.gene_to_transcript
+    );
+
+    // GROUP_BAM2ISOFORM
+    group_bam2isoform(
+        genome_bam,
+        isoform_gff3,
+        tss_tes_stat,
+        gene_dict,
+        transcript_to_junctions,
+        gene_annotation.transcript_dict,
+        chr_to_blocks,
+        genomefa,
+        isoform_parameters,
+        raw_splice_isoform
+    );
+
+    GFFData isoform_annotation = parse_gff_file(isoform_gff3);
+    
+    // get_transcript_seq
+    get_transcript_seq(
+        genomefa,
+        transcript_fa,
+        isoform_annotation,
+        gene_annotation
+    ); // - This does not modify values that are used later (it modifies chr_to_blocks, but only transcript_dict_i and transcript_dict are used later.)
+    return;
+}
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diff --git a/src/main-functions/find_isoform.h b/src/main-functions/find_isoform.h
new file mode 100755
index 0000000..0e19e79
--- /dev/null
+++ b/src/main-functions/find_isoform.h
@@ -0,0 +1,22 @@
+#ifndef FIND_ISOFORM_H
+#define FIND_ISOFORM_H
+
+#include <Rcpp.h>
+
+#include <string>
+
+#include "../classes/Pos.h"
+
+void
+find_isoform
+(
+    const std::string &gff3,
+    const std::string &genome_bam,
+    const std::string &isoform_gff3,
+    const std::string &tss_tes_stat,
+    const std::string &genomefa,
+    const std::string &transcript_fa,
+    const Rcpp::List  &isoform_parameters,
+    const std::string &raw_splice_isoform);
+
+#endif // FIND_ISOFORM_H
\ No newline at end of file