Updated boost to v1.55.0

[rsem.git] / Transcripts.h

diff --git a/Transcripts.h b/Transcripts.h
index 19b025eb2a0868a051db6f0530caf2b9819296a6..033669b740e97737ce4f5f4bc3a25f016a083910 100644 (file)
--- a/Transcripts.h
+++ b/Transcripts.h
@@ -16,7 +16,6 @@
 #include "my_assert.h"
 #include "Transcript.h"
 
-
 class Transcripts {
 public:
        Transcripts(int type = 0) {
@@ -28,7 +27,19 @@ public:
        }
 
        int getM() { return M; }
+
+       // used in shrinking the transcripts
+       void setM(int M) { this->M = M; transcripts.resize(M + 1); } 
+       
+       void move(int from, int to) {
+         assert(from >= to);
+         if (from > to) transcripts[to] = transcripts[from];
+       }
+       
        int getType() { return type; }
+       void setType(int type) { this->type = type; }
+
+       bool isAlleleSpecific() { return type == 2; }
 
        const Transcript& getTranscriptAt(int pos) {
                assert(pos > 0 && pos <= M);
@@ -60,7 +71,7 @@ public:
        void buildMappings(int, char**);
 
 private:
-       int M, type; // type 0 from genome , 1 standalone transcriptome
+       int M, type; // type 0 from genome, 1 standalone transcriptome, 2 allele-specific 
        std::vector<Transcript> transcripts;
 
        std::vector<int> e2i, i2e; // external sid to internal sid, internal sid to external sid
@@ -94,11 +105,11 @@ void Transcripts::buildMappings(int n_targets, char** target_name) {
        std::map<std::string, int> dict;
        std::map<std::string, int>::iterator iter;
 
-       general_assert(n_targets == M, "Number of transcripts does not match! Please check if the reads are aligned to a transcript set (instead of a genome)!");
+       general_assert(n_targets == M, "Number of reference sequences does not match! Please check if the reads are aligned to a transcript set (instead of a genome)!");
 
        dict.clear();
        for (int i = 1; i <= M; i++) {
-               const std::string& tid = transcripts[i].getTranscriptID();
+               const std::string& tid = isAlleleSpecific() ? transcripts[i].getSeqName() : transcripts[i].getTranscriptID();
                iter = dict.find(tid);
                general_assert(iter == dict.end(), tid + " appears more than once!");
                dict[tid] = i;
@@ -108,7 +119,7 @@ void Transcripts::buildMappings(int n_targets, char** target_name) {
        i2e.assign(M + 1, 0);
        for (int i = 0; i < n_targets; i++) {
                iter = dict.find(std::string(target_name[i]));
-               general_assert(iter != dict.end(), "RSEM can not recognize transcript " + cstrtos(target_name[i]) + "!");
+               general_assert(iter != dict.end(), "RSEM can not recognize reference sequence name " + cstrtos(target_name[i]) + "!");
                general_assert(iter->second > 0, "Reference sequence name " + cstrtos(target_name[i]) + " is duplicated!");
                e2i[i + 1] = iter->second;
                i2e[iter->second] = i + 1;