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Searched defs:chromosome_iit (Results 1 – 25 of 41) sorted by relevance

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/dports/biology/gmap/gmap-2020-09-12/src/
H A Dchrnum.c14 Chrnum_to_string (Chrnum_T chrnum, Univ_IIT_T chromosome_iit) { in Chrnum_to_string()
36 Chrnum_to_string_signed (Chrnum_T chrnum, Univ_IIT_T chromosome_iit, bool watsonp) { in Chrnum_to_string_signed()
56 Chrnum_length (Chrnum_T chrnum, Univ_IIT_T chromosome_iit) { in Chrnum_length()
62 Chrnum_offset (Chrnum_T chrnum, Univ_IIT_T chromosome_iit) { in Chrnum_offset()
70 Chrnum_print_position (Univcoord_T position, Univ_IIT_T chromosome_iit) { in Chrnum_print_position()
H A Dparserange.c173 Univ_IIT_T chromosome_iit) { in translate_chromosomepos_universal()
252 Univ_IIT_T chromosome_iit; in convert_to_chrpos() local
273 convert_to_chrpos_iit (Chrpos_T *chrpos, Univ_IIT_T chromosome_iit, Univcoord_T position) { in convert_to_chrpos_iit()
378 Univ_IIT_T chromosome_iit; in Parserange_universal() local
548 char *query, Univ_IIT_T chromosome_iit, Univ_IIT_T contig_iit) { in Parserange_universal_iit()
H A Dmatch.c71 Match_chr (T this, Univ_IIT_T chromosome_iit) { in Match_chr()
133 Univcoord_T position, Univ_IIT_T chromosome_iit) { in Match_new()
175 Match_print_mer (T this, char *queryseq_ptr, Genome_T genome, Univ_IIT_T chromosome_iit, int stage1… in Match_print_mer()
213 Match_print (T this, Univ_IIT_T chromosome_iit) { in Match_print()
H A Dsamread.c531 FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength) { in Samread_parse_acc_and_softclip_fromfile()
987 Univ_IIT_T chromosome_iit, Univcoord_T *chroffsets, int linelength) { in Samread_parse_genomicpos_fromfile()
1308 Samread_parse_mate_genomicpos_fromfile (FILE *fp, Univ_IIT_T chromosome_iit, Univcoord_T *chroffset… in Samread_parse_mate_genomicpos_fromfile()
H A Dindexdb-write.c287 Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit, in Indexdb_count_offsets()
468 …xdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Univ_IIT_T chromosome_iit, in Indexdb_write_offsets()
804 …rite_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp, Univ_IIT_T chromosome_iit, in Indexdb_write_offsets_huge()
1907 FILE *sequence_fp, Univ_IIT_T chromosome_iit, in compute_positions()
2179 FILE *sequence_fp, Univ_IIT_T chromosome_iit, in compute_positions_huge_offsets()
2451 FILE *sequence_fp, Univ_IIT_T chromosome_iit, in Indexdb_write_positions()
2761 FILE *sequence_fp, Univ_IIT_T chromosome_iit, in Indexdb_write_positions_huge_offsets()
H A Dstage1.c486 int genestrand, Univ_IIT_T chromosome_iit, int querylength, in pair_up()
634 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in identify_singles()
750 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in identify_doubles()
912 int expecteddist1, int expecteddist2, Univ_IIT_T chromosome_iit, in identify_triples()
1085 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in identify_matches()
1340 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in stutter()
1452 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in fill_in_5()
1525 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in fill_in_3()
1925 Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end, in find_first_pair()
3310 Univ_IIT_T chromosome_iit, int querylength, in find_good_paths()
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H A Dget-genome.c213 print_two_coords (Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit) { in print_two_coords()
232 Univ_IIT_T chromosome_iit, bool whole_chromosome_p, bool circular_part_p) { in print_sequence()
802 print_interval (char *divstring, int index, IIT_T iit, int ndivs, Univ_IIT_T chromosome_iit, in print_interval()
922 Univ_IIT_T chromosome_iit, contig_iit; in main() local
H A Dgenome-write.c579 fill_circular_chromosomes (UINT4 *genomecomp, Univ_IIT_T chromosome_iit, int circular_typeint) { in fill_circular_chromosomes()
623 … Univ_IIT_T contig_iit, Univ_IIT_T chromosome_iit, int circular_typeint, Genomecomp_T *genomecomp, in genome_write_memory()
785 Univ_IIT_T contig_iit, Univ_IIT_T chromosome_iit, in Genome_write_comp32()
H A Diit_dump.c190 Univ_IIT_T chromosome_iit; in main() local
H A Diit-read-univ.c208 Univ_IIT_genomelength (T chromosome_iit, bool with_circular_alias_p) { in Univ_IIT_genomelength()
234 Univ_IIT_circularp (bool *any_circular_p, T chromosome_iit) { in Univ_IIT_circularp()
260 Univ_IIT_altlocp (Univcoord_T **alias_starts, Univcoord_T **alias_ends, T chromosome_iit, T altscaf… in Univ_IIT_altlocp()
474 Univ_IIT_divint_crosstable (T chromosome_iit, IIT_T iit) { in Univ_IIT_divint_crosstable()
516 Univ_IIT_chrnum_crosstable (T chromosome_iit, IIT_T iit) { in Univ_IIT_chrnum_crosstable()
975 Univ_IIT_dump_contigs (T this, T chromosome_iit, bool directionalp) { in Univ_IIT_dump_contigs()
2361 Univ_IIT_string_from_position (Chrpos_T *chrpos, Univcoord_T position, T chromosome_iit) { in Univ_IIT_string_from_position()
H A Dtrindex.c114 Univ_IIT_T chromosome_iit, transcript_iit; in main() local
H A Dchimera.c110 Chimera_print_sam_tag (Filestring_T fp, T this, Univ_IIT_T chromosome_iit) { in Chimera_print_sam_tag()
815 Univ_IIT_T chromosome_iit, int breakpoint_start, int breakpoint_end) { in find_exonexon_fwd()
953 Univ_IIT_T chromosome_iit, int breakpoint_start, int breakpoint_end) { in find_exonexon_rev()
1093 Univ_IIT_T chromosome_iit, int breakpoint_start, int breakpoint_end) { in Chimera_find_exonexon()
H A Diit_get.c643 print_interval_univ (int index, Univ_IIT_T chromosome_iit) { in print_interval_univ()
787 char *query, char *typestring, Univ_IIT_T *chromosome_iit, char *filename) { in get_matches_univ()
973 Univ_IIT_T chromosome_iit = NULL; in main() local
H A Dsplicetrie_build.c385 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit, in Splicetrie_retrieve_via_splicesites()
806 Univ_IIT_T chromosome_iit, Genome_T genome, Genome_T genomealt, in Splicetrie_retrieve_via_introns()
1861 Univ_IIT_T chromosome_iit, Chrpos_T max_distance, bool distances_observed_p) { in Splicetrie_npartners()
2866 Univ_IIT_T chromosome_iit, IIT_T splicing_iit, int *splicing_divint_crosstable) { in build_via_introns_size()
3125 Univ_IIT_T chromosome_iit, IIT_T splicing_iit, int *splicing_divint_crosstable) { in Splicetrie_build_via_introns()
H A Dgenome.c10572 … Univ_IIT_T chromosome_iit, bool bitbybitp, const char defaultchars[], const char flagchars[]) { in fill_buffer()
10693 Univ_IIT_T chromosome_iit) { in Genome_fill_buffer()
11219 Genome_get_segment (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, in Genome_get_segment()
11247 Genome_get_segment_alt (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, in Genome_get_segment_alt()
11275 Genome_get_segment_snp (T this, Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit, in Genome_get_segment_snp()
H A Dpair.c1413 Univcoord_T chroffset, Univ_IIT_T chromosome_iit, in Pair_print_coordinates()
2094 Univ_IIT_T chromosome_iit) { in donor_score()
2136 Univ_IIT_T chromosome_iit) { in acceptor_score()
2189 Univcoord_T chroffset, Genome_T genome, Univ_IIT_T chromosome_iit, in Pair_print_exonsummary()
3919 Chrnum_T chrnum, bool watsonp, Univ_IIT_T chromosome_iit) { in Pair_print_bedpe()
4167 char *acc_suffix, Univ_IIT_T chromosome_iit) { in Pair_print_m8()
5851 Univ_IIT_T chromosome_iit, Chrpos_T chrpos, Chrpos_T chrlength, in print_sam_line()
7249 Univ_IIT_T chromosome_iit, Sequence_T usersegment, in Pair_print_pslformat_nt()
7339 Univ_IIT_T chromosome_iit, Sequence_T usersegment, in Pair_print_pslformat_pro()
9340 T start, T end, Chrnum_T chrnum, Univ_IIT_T chromosome_iit) { in Pair_print_iit_exon_map()
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H A Dsam_sort.c611 Intlist_T linelengths, int ncells_total, Univ_IIT_T chromosome_iit, in process_without_dups()
832 Intlist_T linelengths, int ncells_total, Univ_IIT_T chromosome_iit, in process_with_dups()
1351 Univ_IIT_T chromosome_iit; in main() local
H A Dsamprint.c72 static Univ_IIT_T chromosome_iit; variable
351 Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p, in SAM_print_nomapping()
1338 int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit, in SAM_print()
1423 Result_T result, Resulttype_T resulttype, Univ_IIT_T chromosome_iit, in SAM_print_paired()
H A Dsnpindex.c639 Univ_IIT_T chromosome_iit, Genome_T genome, in write_offsets()
842 …(UINT4 *snponly_offsetsmeta, UINT4 *snponly_offsetsstrm, IIT_T snps_iit, Univ_IIT_T chromosome_iit, in compute_positions()
1200 Univ_IIT_T chromosome_iit; in main() local
H A Dknownsplicing.c248 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit, in Knownsplicing_retrieve_via_splicesites()
H A Dmatchpool.c161 Univcoord_T diagonal, Univ_IIT_T chromosome_iit) { in Matchpool_push()
H A Dgregion.c180 Gregion_chr (T this, Univ_IIT_T chromosome_iit) { in Gregion_chr()
245 …bool plusp, int genestrand, Univ_IIT_T chromosome_iit, int querystart, int queryend, int queryleng… in Gregion_new()
346 Gregion_new_from_matches (Match_T match5, Match_T match3, int genestrand, Univ_IIT_T chromosome_iit… in Gregion_new_from_matches()
H A Dterminal.c29 static Univ_IIT_T chromosome_iit; variable
H A Dgmapindex.c855 Univ_IIT_T chromosome_iit, bool coord_values_8p) { in write_alt_scaffold_file()
1338 Univ_IIT_T chromosome_iit, contig_iit; in main() local
H A Doutput.c26 static Univ_IIT_T chromosome_iit; variable

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