From 6bcd40fbdd4f33c9660b118201470a9941303341 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20F=C3=BCglistaler?= <andreas.fueglistaler@unifr.ch>
Date: Fri, 8 Apr 2022 14:57:53 +0200
Subject: [PATCH 1/2] allow BamWriter deep copy

---
 src/api/BamWriter.cpp              | 43 ++++++++++++++++++++++++++++--
 src/api/BamWriter.h                |  4 +++
 src/api/internal/bam/BamWriter_p.h |  4 +++
 3 files changed, 49 insertions(+), 2 deletions(-)

diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp
index 6f349ff0..95113e47 100644
--- a/src/api/BamWriter.cpp
+++ b/src/api/BamWriter.cpp
@@ -43,8 +43,47 @@ BamWriter::BamWriter()
 */
 BamWriter::~BamWriter()
 {
-    delete d;
-    d = 0;
+    if (d) delete d;
+    d = nullptr;
+}
+
+/*! \fn BamWriter::BamWriter(const BamWriter& bw)
+    \brief copy constructor, deep copy
+*/
+BamWriter::BamWriter(const BamWriter& bw)
+    : d(nullptr)
+{
+    if (bw.d) d = new BamWriterPrivate(*bw.d);
+}
+
+/*! \fn BamWriter::BamWriter()
+    \brief move constructor, shallow copy
+*/
+BamWriter::BamWriter(BamWriter&& bw) noexcept
+    : d(bw.d)
+{
+    bw.d = nullptr;
+}
+
+/*! \fn BamWriter::operator=(const BamWriter& bw)
+    \brief copy assignement operator, deep copy
+*/
+BamWriter& BamWriter::operator=(const BamWriter& bw)
+{
+    if (d) delete d;
+    if (bw.d) d = new BamWriterPrivate(*bw.d);
+    return *this;
+}
+
+/*! \fn BamWriter::operator=(const BamWriter& bw)
+    \brief move assignement operator, shallow copy
+*/
+BamWriter& BamWriter::operator=(BamWriter&& bw) noexcept
+{
+    if (d) delete d;
+    d    = bw.d;
+    bw.d = nullptr;
+    return *this;
 }
 
 /*! \fn BamWriter::Close()
diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h
index b4c01b5d..26cd9fec 100644
--- a/src/api/BamWriter.h
+++ b/src/api/BamWriter.h
@@ -40,6 +40,10 @@ class API_EXPORT BamWriter
 public:
     BamWriter();
     ~BamWriter();
+    BamWriter(const BamWriter& bw);
+    BamWriter(BamWriter&& bw) noexcept;
+    BamWriter& operator=(const BamWriter& bw);
+    BamWriter& operator=(BamWriter&& bw) noexcept;
 
     // public interface
 public:
diff --git a/src/api/internal/bam/BamWriter_p.h b/src/api/internal/bam/BamWriter_p.h
index 952f5082..583d4355 100644
--- a/src/api/internal/bam/BamWriter_p.h
+++ b/src/api/internal/bam/BamWriter_p.h
@@ -40,6 +40,10 @@ class API_NO_EXPORT BamWriterPrivate
 public:
     BamWriterPrivate();
     ~BamWriterPrivate();
+    BamWriterPrivate(const BamWriterPrivate&) = default;
+    BamWriterPrivate(BamWriterPrivate&&) = default;
+    BamWriterPrivate& operator=(const BamWriterPrivate&) = delete;
+    BamWriterPrivate& operator=(const BamWriterPrivate&&) = delete;
 
     // interface methods
 public:

From 7c3abb4e716e3646ad0f50f1ef5d04b13b3f2877 Mon Sep 17 00:00:00 2001
From: Andreas <andreas.fueglistaler@protonmail.com>
Date: Thu, 17 Nov 2022 16:42:57 +0100
Subject: [PATCH 2/2] add count argument to GetNextSequence to speed up
 sequence reading; remove unnecessary stringstream use

---
 src/utils/bamtools_fasta.cpp | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp
index 11386715..1167d438 100644
--- a/src/utils/bamtools_fasta.cpp
+++ b/src/utils/bamtools_fasta.cpp
@@ -60,7 +60,7 @@ struct Fasta::FastaPrivate
     void Chomp(char* sequence);
     bool GetNameFromHeader(const std::string& header, std::string& name);
     bool GetNextHeader(std::string& header);
-    bool GetNextSequence(std::string& sequence);
+    bool GetNextSequence(std::string& sequence, size_t count = -1);
     bool LoadIndexData();
     bool Rewind();
     bool WriteIndexData();
@@ -387,9 +387,10 @@ bool Fasta::FastaPrivate::GetNextHeader(std::string& header)
     return true;
 }
 
-bool Fasta::FastaPrivate::GetNextSequence(std::string& sequence)
+bool Fasta::FastaPrivate::GetNextSequence(std::string& sequence, size_t count)
 {
 
+    sequence.clear();
     // validate input stream
     if (!IsOpen || feof(Stream)) {
         return false;
@@ -397,8 +398,7 @@ bool Fasta::FastaPrivate::GetNextSequence(std::string& sequence)
 
     // read in sequence
     char buffer[1024];
-    std::ostringstream seqBuffer;
-    while (true) {
+    while (sequence.size() < count) {
 
         char ch = fgetc(Stream);
         ungetc(ch, Stream);
@@ -412,12 +412,9 @@ bool Fasta::FastaPrivate::GetNextSequence(std::string& sequence)
         }
 
         Chomp(buffer);
-        seqBuffer << buffer;
+        sequence.append(buffer);
     }
 
-    // import buffer contents to sequence string
-    sequence = seqBuffer.str();
-
     // return success
     return true;
 }
@@ -459,13 +456,13 @@ bool Fasta::FastaPrivate::GetSequence(const int& refId, const int& start, const
 
         // retrieve full sequence
         std::string fullSequence;
-        if (!GetNextSequence(fullSequence)) {
+        const int seqLength = (stop - start) + 1;
+        if (!GetNextSequence(fullSequence, stop + 1)) {
             std::cerr << "FASTA error : could not retrieve sequence from FASTA file" << std::endl;
             return false;
         }
 
         // set sub-sequence & return success
-        const int seqLength = (stop - start) + 1;
         sequence = fullSequence.substr(start, seqLength);
         return true;
     }