refine stdin/stdout modes

src/options.cpp

@@ -18,17 +18,13 @@ Options::Options(){
 }
 
 bool Options::isFastqFile(string filename) {
-    if(filename == "/dev/stdin" || filename=="/dev/stdout")
-        return true;
     if(ends_with(filename, ".fq") || ends_with(filename, ".fastq") || ends_with(filename, ".fq.gz")|| ends_with(filename, ".fastq.gz"))
         return true;
 
     return false;
 }
 
 bool Options::isRfqFile(string filename) {
-    if(filename == "/dev/stdin" || filename=="/dev/stdout")
-        return true;
     if(ends_with(filename, ".rfq") || ends_with(filename, ".rfq.xz"))
         return true;
 
@@ -62,8 +58,8 @@ bool Options::validate() {
     if(compressMode == true) {
         if(!out2.empty())
             error_exit("In compress mode, only one RFQ output file is allowed, but you specified <out2>");
-        if(!isRfqFile(out1))
-            error_exit("In compress mode, the output should be a RFQ file. Expect a .rfq file, but got " + out1);
+        //if(!isRfqFile(out1))
+        //    error_exit("In compress mode, the output should be a RFQ file. Expect a .rfq file, but got " + out1);
         if(isFastqFile(out1))
             error_exit("In compress mode, the output should not be a FASTQ file. Expect a .rfq or .rfq.xz file, but got " + out1);
         if(isRfqFile(in1))

src/repaq.cpp

@@ -34,9 +34,9 @@ void Repaq::decompress(){
     RfqHeader* header = new RfqHeader();
     header->read(input);
 
-    if(header->mFlags & BIT_PAIRED_END) {
+    /*if(header->mFlags & BIT_PAIRED_END) {
         error_exit("The input RFQ file was encoded by paired-end FASTQ, you should specify <out1> and <out2>");
-    }
+    }*/
 
     codec.setHeader(header);