remove uses of std::cout and puts from C++ code

mritchielab · Jul 5, 2023 · 8f17448 · 8f17448
1 parent d5dfadd
commit 8f17448
Show file tree

Hide file tree

Showing 3 changed files with 15 additions and 15 deletions.
diff --git a/src/main-functions/get_transcript_seq.cpp b/src/main-functions/get_transcript_seq.cpp
@@ -147,7 +147,7 @@ get_transcript_seq(
 
  fa_dict[transcript] = transcript_seq;
  if (global_seq_dict.find(transcript_seq) != global_seq_dict.end()) {
- std::cout << "Duplicate transcript sequence: " << global_seq_dict[transcript_seq] << ", " << transcript << "\n";
+ Rcpp::Rcout << "Duplicate transcript sequence: " << global_seq_dict[transcript_seq] << ", " << transcript << "\n";
  } else {
  global_seq_dict[transcript_seq] = transcript;
  }

diff --git a/src/utility/bam.c b/src/utility/bam.c
@@ -44,15 +44,15 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
  return str.s;
 }
 
-int bam_view1(const bam_header_t *header, const bam1_t *b)
-{
- char *s = bam_format1(header, b);
- int ret = -1;
- if (!s) return -1;
- if (puts(s) != EOF) ret = 0;
- free(s);
- return ret;
-}
+// int bam_view1(const bam_header_t *header, const bam1_t *b)
+// {
+//  char *s = bam_format1(header, b);
+//  int ret = -1;
+//  if (!s) return -1;
+//  if (puts(s) != EOF) ret = 0;
+//  free(s);
+//  return ret;
+// }
 
 int bam_validate1(const bam_header_t *header, const bam1_t *b)
 {

diff --git a/src/utility/bam.h b/src/utility/bam.h
@@ -382,11 +382,11 @@ extern "C" {
  */
  char *bam_format1(const bam_header_t *header, const bam1_t *b);
 
- /*!
- @abstract Formats a BAM record and writes it and \n to stdout
- @return 0 if successful, -1 on error
- */
- int bam_view1(const bam_header_t *header, const bam1_t *b);
+ // /*!
+ //  @abstract Formats a BAM record and writes it and \n to stdout
+ //  @return 0 if successful, -1 on error
+ //  */
+ // int bam_view1(const bam_header_t *header, const bam1_t *b);
 
  /*!
  @abstract Check whether a BAM record is plausibly valid