From 2bd8699bbb8e2f1fb0677d44049bddbb7fe39419 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20F=C3=BCglistaler?= <andreas.fueglistaler@unifr.ch>
Date: Fri, 4 Mar 2022 11:11:01 +0100
Subject: [PATCH] make Fasta Length available

---
 src/api/BamReader.h          |  1 -
 src/utils/bamtools_fasta.cpp | 26 ++++++++++++++++++++++++++
 src/utils/bamtools_fasta.h   |  1 +
 3 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index e213713a..b73ad4dd 100644
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -55,7 +55,6 @@ class API_EXPORT BamReader
                    const int& rightPosition);
     int64_t Tell() const;
 
-
     // ----------------------
     // access alignment data
     // ----------------------
diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp
index 80096d62..11386715 100644
--- a/src/utils/bamtools_fasta.cpp
+++ b/src/utils/bamtools_fasta.cpp
@@ -52,6 +52,7 @@ struct Fasta::FastaPrivate
     bool CreateIndex(const std::string& indexFilename);
     bool GetBase(const int& refId, const int& position, char& base);
     bool GetSequence(const int& refId, const int& start, const int& stop, std::string& sequence);
+    bool GetLength(const int& refId, int& length);
     bool Open(const std::string& filename, const std::string& indexFilename);
 
     // internal methods
@@ -509,6 +510,26 @@ bool Fasta::FastaPrivate::GetSequence(const int& refId, const int& start, const
     return true;
 }
 
+bool Fasta::FastaPrivate::GetLength(const int& refId, int& length)
+{
+    // make sure FASTA file is open
+    if (!IsOpen) {
+        std::cerr << "FASTA error : file not open for reading\n";
+        return false;
+    }
+
+    // make sure index if available
+    if (!HasIndex && Index.empty()) {
+        std::cerr << "FASTA error : could not read from index file\n";
+        return false;
+    }
+
+    length = Index.at(refId).Length;
+
+    // return success
+    return true;
+}
+
 bool Fasta::FastaPrivate::LoadIndexData()
 {
 
@@ -670,3 +691,8 @@ bool Fasta::Open(const std::string& filename, const std::string& indexFilename)
 {
     return d->Open(filename, indexFilename);
 }
+
+bool Fasta::GetLength(const int& refId, int& length)
+{
+    return d->GetLength(refId, length);
+}
diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h
index 3b306233..7e9b811c 100644
--- a/src/utils/bamtools_fasta.h
+++ b/src/utils/bamtools_fasta.h
@@ -32,6 +32,7 @@ class UTILS_EXPORT Fasta
 public:
     bool GetBase(const int& refID, const int& position, char& base);
     bool GetSequence(const int& refId, const int& start, const int& stop, std::string& sequence);
+    bool GetLength(const int& refId, int& length);
 
     // index-handling methods
 public: