Adding an indication that certain classes will be deprecated within htslib_wrapper so we can prevent name clashes

Author: andrewdavidsmith

htslib_wrapper.cpp

@@ -1,4 +1,5 @@
 /* Part of SMITHLAB_CPP software
+ * This code will be replaced soon
  *
  * Copyright (C) 2013-2019 University of Southern California and
  *                         Andrew D. Smith
@@ -34,7 +35,7 @@ using std::runtime_error;
 
 char check_htslib_wrapper() {return 1;}
 
-SAMReader::SAMReader(const string &fn, const string &mpr) :
+SAMReader_deprecated::SAMReader_deprecated(const string &fn, const string &mpr) :
   filename(fn), mapper(mpr), good(true) {
 
   if (!(hts = hts_open(filename.c_str(), "r")))
@@ -56,7 +57,7 @@ SAMReader::SAMReader(const string &fn, const string &mpr) :
     throw runtime_error("mapper not supported: " + mapper);
 }
 
-SAMReader::~SAMReader() {
+SAMReader_deprecated::~SAMReader_deprecated() {
   if (hdr) {
     bam_hdr_destroy(hdr);
     hdr = 0;
@@ -74,7 +75,7 @@ SAMReader::~SAMReader() {
 
 
 bool
-SAMReader::get_SAMRecord(const string &str, SAMRecord &samr) {
+SAMReader_deprecated::get_SAMRecord(const string &str, SAMRecord &samr) {
   if (mapper == "bsmap")
     return get_SAMRecord_bsmap(str, samr);
   else if (mapper == "bismark")
@@ -88,8 +89,8 @@ SAMReader::get_SAMRecord(const string &str, SAMRecord &samr) {
   return false;
 }
 
-SAMReader&
-operator>>(SAMReader &reader, SAMRecord &aln) {
+SAMReader_deprecated&
+operator>>(SAMReader_deprecated &reader, SAMRecord &aln) {
   int rd_ret = 0;
   if ((rd_ret = sam_read1(reader.hts, reader.hdr, reader.b)) >= 0) {
     int fmt_ret = 0;
@@ -145,7 +146,7 @@ bsmap_get_strand(const string &strand_str, string &strand, string &bs_forward) {
 }
 
 bool
-SAMReader::get_SAMRecord_bsmap(const string &str, SAMRecord &samr) {
+SAMReader_deprecated::get_SAMRecord_bsmap(const string &str, SAMRecord &samr) {
 
   cerr << "WARNING: "<< "[BSMAP Converter] test "
        << "version: may contain bugs" << endl;
@@ -217,7 +218,7 @@ get_mismatch_bismark(const string &edit_distance_str,
 }
 
 bool
-SAMReader::get_SAMRecord_bismark(const string &str, SAMRecord &samr) {
+SAMReader_deprecated::get_SAMRecord_bismark(const string &str, SAMRecord &samr) {
   string name, chrom, CIGAR, mate_name, seq, qual, strand_str,
     edit_distance_str, mismatch_str, meth_call_str,
     read_conv_str, genome_conv_str;
@@ -283,7 +284,7 @@ class BSSEEKERFLAG : public FLAG {
 };
 
 bool
-SAMReader::get_SAMRecord_bsseeker(const string &str, SAMRecord &samr) {
+SAMReader_deprecated::get_SAMRecord_bsseeker(const string &str, SAMRecord &samr) {
 
   string name, chrom, CIGAR, mate_name, seq, qual, orientation_str,
     conversion_str, mismatch_str, mismatch_type_str, seq_genome_str;
@@ -336,7 +337,7 @@ class GENERALFLAG : public FLAG {
 };
 
 bool
-SAMReader::get_SAMRecord_general(const string &str, SAMRecord &samr) {
+SAMReader_deprecated::get_SAMRecord_general(const string &str, SAMRecord &samr) {
   string name, chrom, CIGAR, mate_name, seq, qual;
   size_t flag, start, mapq_score, mate_start;
   int seg_len;

htslib_wrapper.hpp

@@ -1,5 +1,6 @@
 /*
  * Part of SMITHLAB_CPP software
+ * This code will be replaced soon
  *
  * Copyright (C) 2019 Meng Zhou and Andrew Smith
  *
@@ -61,15 +62,15 @@ struct SAMRecord {
   std::string get_chrom() const {return mr.r.get_chrom();}
 };
 
-class SAMReader {
+class SAMReader_deprecated {
 public:
-  SAMReader(const std::string &filename, const std::string &mapper);
-  ~SAMReader();
+  SAMReader_deprecated(const std::string &filename, const std::string &mapper);
+  ~SAMReader_deprecated();
 
   operator bool() const {return good;}
 
-  friend SAMReader &
-  operator>>(SAMReader& sam_stream, SAMRecord &samr);
+  friend SAMReader_deprecated &
+  operator>>(SAMReader_deprecated& sam_stream, SAMRecord &samr);
 
 private:
   // internal methods
@@ -94,7 +95,7 @@ class SAMReader {
   bam1_t *b;
 };
 
-SAMReader &
-operator>>(SAMReader& sam_stream, SAMRecord &samr);
+SAMReader_deprecated &
+operator>>(SAMReader_deprecated& sam_stream, SAMRecord &samr);
 
 #endif