| 605 | typedef struct state_struct state_t; |
| 606 | |
| 607 | state_t * makeState () |
| 608 | { |
| 609 | state_t * s = new state_t(); |
| 610 | s->inputFile = stdin; |
| 611 | s->inputFileName = (char *)"stdin"; |
| 612 | s->outputFile = stdout; |
| 613 | s->outputFileName = (char *)"stdout"; |
| 614 | s->discordantFile = NULL; |
| 615 | s->discordantFileName = (char *)""; |
| 616 | s->splitterFile = NULL; |
| 617 | s->splitterFileName = (char *)""; |
| 618 | s->unmappedClippedFile = NULL; |
| 619 | s->unmappedClippedFileName = (char *)""; |
| 620 | s->sigs = NULL; |
| 621 | s->minNonOverlap = 20; |
| 622 | s->maxSplitCount = 2; |
| 623 | s->minIndelSize = 50; |
| 624 | s->maxUnmappedBases = 50; |
| 625 | s->minClip = 20; |
| 626 | s->maxReadLength = 500; |
| 627 | s->acceptDups = false; |
| 628 | s->excludeDups = false; |
| 629 | s->removeDups = false; |
| 630 | s->addMateTags = false; |
| 631 | s->compatMode = false; |
| 632 | s->ignoreUnmated = false; |
| 633 | s->quiet = false; |
| 634 | // Start this as -1 to indicate we don't know yet. |
| 635 | // Once we are outputting our first line, we will decide. |
| 636 | s->unmappedFastq = -1; |
| 637 | // Used as a temporary location for ptrs to splitter for sort routine. |
| 638 | s->splitterArrayMaxSize = 1000; |
| 639 | s->splitterArray = (splitLine_t **)(malloc(s->splitterArrayMaxSize * sizeof(splitLine_t *))); |
| 640 | return s; |
| 641 | } |
| 642 | |
| 643 | void deleteState(state_t * s) |
| 644 | { |