Allowed for a subset of reference sequences to be declared in an input SAM/BAM file...

[rsem.git] / SamParser.h

diff --git a/SamParser.h b/SamParser.h
index e91f9c379539fc7ada0f8682bcfc7c957489d67f..81d4097cf0033dee55d012abeaf8ea106120b9d9 100644 (file)
--- a/SamParser.h
+++ b/SamParser.h
@@ -25,7 +25,7 @@
 
 class SamParser {
 public:
 
 class SamParser {
 public:

-       SamParser(char, const char*, Transcripts&, const char* = 0);
+       SamParser(char, const char*, const char*, Transcripts&, const char*);

        ~SamParser();
 
        /**
        ~SamParser();
 
        /**


@@ -80,7 +80,7 @@ private:
 char SamParser::rtTag[STRLEN] = ""; // default : no tag, thus no Type 2 reads
 
 // aux, if not 0, points to the file name of fn_list
 char SamParser::rtTag[STRLEN] = ""; // default : no tag, thus no Type 2 reads
 
 // aux, if not 0, points to the file name of fn_list

-SamParser::SamParser(char inpType, const char* inpF, Transcripts& transcripts, const char* aux)
+SamParser::SamParser(char inpType, const char* inpF, const char* aux, Transcripts& transcripts, const char* imdName)

        : transcripts(transcripts)
 {
        switch(inpType) {
        : transcripts(transcripts)
 {
        switch(inpType) {


@@ -93,7 +93,7 @@ SamParser::SamParser(char inpType, const char* inpF, Transcripts& transcripts, c
        header = sam_in->header;
        general_assert(header != 0, "Fail to parse sam header!");
 
        header = sam_in->header;
        general_assert(header != 0, "Fail to parse sam header!");
 

-       transcripts.buildMappings(header->n_targets, header->target_name);
+       transcripts.buildMappings(header->n_targets, header->target_name, imdName);

 
        b = bam_init1();
        b2 = bam_init1();
 
        b = bam_init1();
        b2 = bam_init1();