| 2664 | } |
| 2665 | |
| 2666 | InputFormat getInputFormat(std::string const& inputFormat) |
| 2667 | { |
| 2668 | if (inputFormat.compare("sam")==0 || inputFormat.compare("SAM")==0) { |
| 2669 | return SAM_INPUT_FORMAT; |
| 2670 | } |
| 2671 | |
| 2672 | if (inputFormat.compare("bam")==0 || inputFormat.compare("BAM")==0) { |
| 2673 | return SAM_INPUT_FORMAT; |
| 2674 | } |
| 2675 | |
| 2676 | if (inputFormat.compare("eland")==0 || inputFormat.compare("Eland")==0) { |
| 2677 | return ELAND_INPUT_FORMAT; |
| 2678 | } |
| 2679 | |
| 2680 | if (inputFormat.compare("bowtie")==0 || inputFormat.compare("Bowtie")==0) { |
| 2681 | return BOWTIE_INPUT_FORMAT; |
| 2682 | } |
| 2683 | |
| 2684 | if (inputFormat.compare("psl")==0 || inputFormat.compare("BLAT")==0) { |
| 2685 | return PSL_INPUT_FORMAT; |
| 2686 | } |
| 2687 | |
| 2688 | if (inputFormat.compare("arachne")==0 || inputFormat.compare("BED")==0 || inputFormat.compare("bed")==0 || inputFormat.compare("ARACHNE")==0) { |
| 2689 | return ARACHNE_BED_INPUT_FORMAT; |
| 2690 | } |
| 2691 | |
| 2692 | if (inputFormat.compare("SOAP")==0 || inputFormat.compare("soap")==0 || inputFormat.compare("Soap")==0) { |
| 2693 | return SOAP_INPUT_FORMAT; |
| 2694 | } |
| 2695 | |
| 2696 | if (inputFormat.compare("pileup")==0 || inputFormat.compare("SAMtools pileup")==0) { |
| 2697 | return SAM_PILEUP_INPUT_FORMAT; |
| 2698 | } |
| 2699 | |
| 2700 | return UNKNOWN_INPUT_FORMAT; |
| 2701 | } |
| 2702 | |
| 2703 | char* getLine(char* buffer, int buffer_size, FILE* stream, std::string& line) |
| 2704 | { |
no test coverage detected