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NVBIO
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NVBIO
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Definition at line 622 of file cram_structs.h.
#include <cram_structs.h>
Public Members | |
| cram_FILE * | fp |
| int | mode |
| int | version |
| cram_file_def * | file_def |
| SAM_hdr * | header |
| char * | prefix |
| int | record_counter |
| int | slice_num |
| int | err |
| cram_container * | ctr |
| int | first_base |
| int | last_base |
| refs_t * | refs |
| char * | ref |
| char * | ref_free |
| int | ref_id |
| int | ref_start |
| int | ref_end |
| char * | ref_fn |
| int | level |
| cram_metrics * | m [7] |
| int | decode_md |
| int | verbose |
| int | seqs_per_slice |
| int | slices_per_container |
| int | embed_ref |
| int | no_ref |
| int | ignore_md5 |
| int | use_bz2 |
| int | shared_ref |
| cram_range | range |
| unsigned int | bam_flag_swap [0x1000] |
| unsigned int | cram_flag_swap [0x1000] |
| unsigned char | L1 [256] |
| unsigned char | L2 [256] |
| char | cram_sub_matrix [32][32] |
| int | index_sz |
| cram_index * | index |
| off_t | first_container |
| int | eof |
| int | last_slice |
| int | multi_seq |
| int | unsorted |
| int | empty_container |
| int | own_pool |
| t_pool * | pool |
| t_results_queue * | rqueue |
| pthread_mutex_t | metrics_lock |
| pthread_mutex_t | ref_lock |
| spare_bams * | bl |
| pthread_mutex_t | bam_list_lock |
| void * | job_pending |
| int | ooc |
| unsigned int cram_fd::bam_flag_swap[0x1000] |
Definition at line 669 of file cram_structs.h.
| pthread_mutex_t cram_fd::bam_list_lock |
Definition at line 691 of file cram_structs.h.
| spare_bams* cram_fd::bl |
Definition at line 690 of file cram_structs.h.
| unsigned int cram_fd::cram_flag_swap[0x1000] |
Definition at line 670 of file cram_structs.h.
| char cram_fd::cram_sub_matrix[32][32] |
Definition at line 673 of file cram_structs.h.
| cram_container* cram_fd::ctr |
Definition at line 639 of file cram_structs.h.
| int cram_fd::decode_md |
Definition at line 657 of file cram_structs.h.
| int cram_fd::embed_ref |
Definition at line 661 of file cram_structs.h.
| int cram_fd::empty_container |
Definition at line 682 of file cram_structs.h.
| int cram_fd::eof |
Definition at line 678 of file cram_structs.h.
| int cram_fd::err |
Definition at line 632 of file cram_structs.h.
| cram_file_def* cram_fd::file_def |
Definition at line 626 of file cram_structs.h.
| int cram_fd::first_base |
Definition at line 642 of file cram_structs.h.
| off_t cram_fd::first_container |
Definition at line 677 of file cram_structs.h.
| cram_FILE* cram_fd::fp |
Definition at line 623 of file cram_structs.h.
| SAM_hdr* cram_fd::header |
Definition at line 627 of file cram_structs.h.
| int cram_fd::ignore_md5 |
Definition at line 663 of file cram_structs.h.
| cram_index* cram_fd::index |
Definition at line 676 of file cram_structs.h.
| int cram_fd::index_sz |
Definition at line 675 of file cram_structs.h.
| void* cram_fd::job_pending |
Definition at line 692 of file cram_structs.h.
| unsigned char cram_fd::L1[256] |
Definition at line 671 of file cram_structs.h.
| unsigned char cram_fd::L2[256] |
Definition at line 672 of file cram_structs.h.
| int cram_fd::last_base |
Definition at line 642 of file cram_structs.h.
| int cram_fd::last_slice |
Definition at line 679 of file cram_structs.h.
| int cram_fd::level |
Definition at line 653 of file cram_structs.h.
| cram_metrics* cram_fd::m[7] |
Definition at line 654 of file cram_structs.h.
| pthread_mutex_t cram_fd::metrics_lock |
Definition at line 688 of file cram_structs.h.
| int cram_fd::mode |
Definition at line 624 of file cram_structs.h.
| int cram_fd::multi_seq |
Definition at line 680 of file cram_structs.h.
| int cram_fd::no_ref |
Definition at line 662 of file cram_structs.h.
| int cram_fd::ooc |
Definition at line 693 of file cram_structs.h.
| int cram_fd::own_pool |
Definition at line 685 of file cram_structs.h.
| t_pool* cram_fd::pool |
Definition at line 686 of file cram_structs.h.
| char* cram_fd::prefix |
Definition at line 629 of file cram_structs.h.
| cram_range cram_fd::range |
Definition at line 666 of file cram_structs.h.
| int cram_fd::record_counter |
Definition at line 630 of file cram_structs.h.
| char* cram_fd::ref |
Definition at line 646 of file cram_structs.h.
| int cram_fd::ref_end |
Definition at line 649 of file cram_structs.h.
| char* cram_fd::ref_fn |
Definition at line 650 of file cram_structs.h.
| char * cram_fd::ref_free |
Definition at line 646 of file cram_structs.h.
| int cram_fd::ref_id |
Definition at line 647 of file cram_structs.h.
| pthread_mutex_t cram_fd::ref_lock |
Definition at line 689 of file cram_structs.h.
| int cram_fd::ref_start |
Definition at line 648 of file cram_structs.h.
| refs_t* cram_fd::refs |
Definition at line 645 of file cram_structs.h.
| t_results_queue* cram_fd::rqueue |
Definition at line 687 of file cram_structs.h.
| int cram_fd::seqs_per_slice |
Definition at line 659 of file cram_structs.h.
| int cram_fd::shared_ref |
Definition at line 665 of file cram_structs.h.
| int cram_fd::slice_num |
Definition at line 631 of file cram_structs.h.
| int cram_fd::slices_per_container |
Definition at line 660 of file cram_structs.h.
| int cram_fd::unsorted |
Definition at line 681 of file cram_structs.h.
| int cram_fd::use_bz2 |
Definition at line 664 of file cram_structs.h.
| int cram_fd::verbose |
Definition at line 658 of file cram_structs.h.
| int cram_fd::version |
Definition at line 625 of file cram_structs.h.
1.8.4