1 /* $Id: output.h 222398 2020-04-14 21:23:56Z twu $ */ 2 #ifndef OUTPUT_INCLUDED 3 #define OUTPUT_INCLUDED 4 5 typedef enum {STD_OUTPUT, SAM_OUTPUT, M8_OUTPUT} Outputtype_T; 6 7 typedef enum {SIMPLE, SUMMARY, ALIGNMENT, COMPRESSED, CONTINUOUS, CONTINUOUS_BY_EXON, 8 EXONS_CDNA, EXONS_GENOMIC, EXONS_CDNA_WINTRONS, EXONS_GENOMIC_WINTRONS, 9 MASK_INTRONS, MASK_UTR_INTRONS, CDNA, PROTEIN_GENOMIC, 10 PSL_NT, PSL_PRO, GFF3_GENE, GFF3_MATCH_CDNA, GFF3_MATCH_EST, BEDPE, 11 SAM, COORDS, SPLICESITES, INTRONS, MAP_RANGES, MAP_EXONS} Printtype_T; 12 13 #include "types.h" 14 #include "bool.h" 15 #include "genomicpos.h" 16 #include "iit-read-univ.h" 17 #include "iit-read.h" 18 #include "filestring.h" 19 20 #include "request.h" 21 #include "mem.h" /* To get MEMUSAGE */ 22 23 #ifdef GSNAP 24 #include "resulthr.h" 25 #else 26 #include "result.h" 27 #include "sequence.h" 28 #endif 29 30 extern void 31 Output_setup (Univ_IIT_T chromosome_iit_in, 32 bool nofailsp_in, bool failsonlyp_in, bool quiet_if_excessive_p_in, int maxpaths_report_in, 33 char *failedinput_root_in, int quality_shift_in, 34 #ifdef GSNAP 35 Outputtype_T output_type_in, bool invert_first_p_in, bool invert_second_p_in, 36 #else 37 Printtype_T printtype_in, int invertmode_in, int wraplength_in, int ngap_in, 38 bool nointronlenp_in, bool sam_paired_p_in, int cds_startpos_in, 39 bool fulllengthp_in, bool truncatep_in, bool strictp_in, bool checksump_in, 40 41 Genome_T genome_in, Sequence_T usersegment_in, char *user_genomicseg_in, 42 char *dbversion_in, char *chrsubset_name_in, 43 Univ_IIT_T contig_iit_in, IIT_T altstrain_iit_in, bool chimeras_allowed_p_in, 44 IIT_T map_iit_in, int *map_divint_crosstable_in, bool map_exons_p_in, 45 bool map_bothstrands_p_in, int nflanking_in, bool print_comment_p_in, 46 #endif 47 char *sam_read_group_id_in); 48 49 50 #ifdef GSNAP 51 extern Filestring_T 52 Output_filestring_fromresult (Filestring_T *fp_failedinput, Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2, 53 Result_T result, Request_T request); 54 #else 55 extern Filestring_T 56 Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Request_T request, 57 Sequence_T headerseq); 58 #endif 59 60 61 #endif 62 63