////////////////////////////////////////////////////////////////////////// Struct for processing state //////////////////////////////////////////////////////////////////////////
| 568 | // Struct for processing state |
| 569 | /////////////////////////////////////////////////////////////////////////////// |
| 570 | struct state_struct |
| 571 | { |
| 572 | char * inputFileName; |
| 573 | FILE * inputFile; |
| 574 | char * outputFileName; |
| 575 | FILE * outputFile; |
| 576 | FILE * discordantFile; |
| 577 | char * discordantFileName; |
| 578 | FILE * splitterFile; |
| 579 | char * splitterFileName; |
| 580 | FILE * unmappedClippedFile; |
| 581 | char * unmappedClippedFileName; |
| 582 | sigSet_t * sigs; |
| 583 | seqMap_t seqs; |
| 584 | UINT32 * seqLens; |
| 585 | UINT64 * seqOffs; |
| 586 | splitLine_t ** splitterArray; |
| 587 | int splitterArrayMaxSize; |
| 588 | UINT32 sigArraySize; |
| 589 | int binCount; |
| 590 | int minNonOverlap; |
| 591 | int maxReadLength; |
| 592 | int maxSplitCount; |
| 593 | int minIndelSize; |
| 594 | int maxUnmappedBases; |
| 595 | int minClip; |
| 596 | int unmappedFastq; |
| 597 | bool acceptDups; |
| 598 | bool excludeDups; |
| 599 | bool removeDups; |
| 600 | bool addMateTags; |
| 601 | bool compatMode; |
| 602 | bool ignoreUnmated; |
| 603 | bool quiet; |
| 604 | }; |
| 605 | typedef struct state_struct state_t; |
| 606 | |
| 607 | state_t * makeState () |
nothing calls this directly
no outgoing calls
no test coverage detected