X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=synthesisRef.cpp;h=aa0d473b6537088fcb820f246de9898fa1864ef4;hb=5a1c0c7e480ffda84f83d224246c754a4761500f;hp=005cf95fee33e1031077a5993b1c771f1e4d6579;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/synthesisRef.cpp b/synthesisRef.cpp
index 005cf95..aa0d473 100644
--- a/synthesisRef.cpp
+++ b/synthesisRef.cpp
@@ -17,8 +17,8 @@ int M;
 map<string, string> name2seq;
 map<string, string>::iterator iter;
 
-Transcripts transcripts;
-char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN];
+Transcripts transcripts(1); // no genome, just transcript set
+char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN], chromListF[STRLEN];
 
 bool hasMappingFile;
 char mappingFile[STRLEN];
@@ -56,12 +56,13 @@ char check(char c) {
 }
 
 void writeResults(char* refName) {
-	ofstream fout;
+	ofstream fout, fout2;
 	string cur_gene_id, name;
 
 	sprintf(groupF, "%s.grp", refName);
 	sprintf(tiF, "%s.ti", refName);
 	sprintf(refFastaF, "%s.transcripts.fa", refName);
+	sprintf(chromListF, "%s.chrlist", refName);
 
 	transcripts.writeTo(tiF);
 	if (verbose) { printf("Transcript Information File is generated!\n"); }
@@ -79,7 +80,7 @@ void writeResults(char* refName) {
 	fout.close();
 	if (verbose) { printf("Group File is generated!\n"); }
 
-	// We have to generate this .transcripts.fa, even reference_file is only one. Reason : polyA choice 2, need ">transcript_id"
+	fout2.open(chromListF);
 	fout.open(refFastaF);
 	for (int i = 1; i <= M; i++) {
 		name = transcripts.getTranscriptAt(i).getTranscriptID();
@@ -90,13 +91,20 @@ void writeResults(char* refName) {
 		}
 		fout<<">"<<name<<endl;
 		fout<<iter->second<<endl;
+
+		fout2<<name<<'\t'<<iter->second.length()<<endl;
 	}
 	fout.close();
-	if (verbose) { printf("Extracted Sequences File is generated!\n"); }
+	fout2.close();
+	
+	if (verbose) { 
+	  printf("Chromosome List File is generated!\n"); 
+	  printf("Extracted Sequences File is generated!\n"); 
+	}
 }
 
 int main(int argc, char* argv[]) {
-	if (argc < 5 || (hasMappingFile = atoi(argv[3])) && argc < 6) {
+  if (argc < 5 || ((hasMappingFile = atoi(argv[3])) && argc < 6)) {
 		printf("Usage: synthesisRef refName quiet hasMappingFile [mappingFile] reference_file_1 [reference_file_2 ...]\n");
 		exit(-1);
 	}
@@ -110,7 +118,6 @@ int main(int argc, char* argv[]) {
 	ifstream fin;
 	string line, gseq;
 	string seqname, gene_id;
-	void* pt;
 
 	vector<Interval> vec;
 
@@ -119,13 +126,13 @@ int main(int argc, char* argv[]) {
 	for (int i = start; i < argc; i++) {
 		fin.open(argv[i]);
 		if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[i]); exit(-1); }
-		pt = getline(fin, line);
-		while (pt != 0 && line[0] == '>') {
+		getline(fin, line);
+		while ((fin) && (line[0] == '>')) {
 			istringstream strin(line.substr(1));
 			strin>>seqname;
 
 			gseq = "";
-			while((pt = getline(fin, line)) && line[0] != '>') {
+			while((getline(fin, line)) && (line[0] != '>')) {
 			    gseq += line;
 			}