| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | compress-write.c | 453 high = genomecomp[ptr]; in Compress_update_memory()
454 low = genomecomp[ptr+1]; in Compress_update_memory()
455 flags = genomecomp[ptr+2]; in Compress_update_memory()
475 high = genomecomp[ptr]; in Compress_update_memory()
476 low = genomecomp[ptr+1]; in Compress_update_memory()
477 flags = genomecomp[ptr+2]; in Compress_update_memory()
505 high = genomecomp[ptr]; in Compress_update_memory()
785 Genomecomp_T *genomecomp; in Compress_create_blocks_comp() local
805 return genomecomp; in Compress_create_blocks_comp()
819 high = genomecomp[ptr]; in Compress_create_blocks_bits()
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| H A D | genome-write.c | 696 fill_x_memory(genomecomp,maxposition,startposition); in genome_write_memory()
700 fill_x_memory(genomecomp,leftposition,rightposition + 1); in genome_write_memory()
714 fill_x_memory(genomecomp,maxposition,rightposition + 1); in genome_write_memory()
776 FWRITE_UINTS(genomecomp,nuint4,refgenome_fp); in genome_write_memory()
791 Genomecomp_T *genomecomp; in Genome_write_comp32() local
838 if (genomecomp == NULL) { in Genome_write_comp32()
851 genomecomp[nuint4-5] = 0xFFFFFFFF; in Genome_write_comp32()
852 genomecomp[nuint4-4] = 0xFFFFFFFF; in Genome_write_comp32()
853 genomecomp[nuint4-3] = 0xFFFFFFFF; in Genome_write_comp32()
863 genomecomp,nuint4,nmessages); in Genome_write_comp32()
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| H A D | compress-write.h | 17 Compress_update_memory (int nbadchars, Genomecomp_T *genomecomp, char *gbuffer, Univcoord_T startpo…
28 Compress_create_blocks_bits (Genomecomp_T *genomecomp, Univcoord_T genomelength);
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| H A D | gmap.c | 207 static Genome_T genomecomp = NULL; variable
4747 Oligoindex_pmap_setup(genomecomp); in worker_mpi_process()
4929 Oligoindex_pmap_setup(genomecomp); in single_thread()
5100 Oligoindex_pmap_setup(genomecomp); in worker_thread()
6770 genomecomp = (Genome_T) NULL; in main()
6784 genomecomp = (Genome_T) NULL; in main()
6985 Oligoindex_pmap_setup(genomecomp); in main()
6991 } else if (genomecomp != NULL) { in main()
6999 Oligoindex_pmap_setup(genomecomp); in main()
7271 } else if (genomecomp != NULL) { in main()
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| H A D | gsnap.c | 225 static Genome_T genomecomp = NULL; variable
3088 … genomecomp = Genome_new(genomesubdir,genome_fileroot,/*alt_root*/NULL,/*genometype*/GENOME_OLIGOS, in worker_setup()
3094 … genomecomp = Genome_new(genomesubdir,genome_fileroot,/*alt_root*/NULL,/*genometype*/GENOME_OLIGOS, in worker_setup()
3119 … genomecomp = Genome_new(genomesubdir,genome_fileroot,/*alt_root*/NULL,/*genometype*/GENOME_OLIGOS, in worker_setup()
3130 Genome_setup(genomecomp,genomecomp_alt,genomelength,mode,circular_typeint); in worker_setup()
3312 genomecomp,genomecomp_alt,shortsplicedist); in worker_setup()
3495 chromosome_iit,nchromosomes,genomecomp,genomebits,genomebits_alt, in worker_setup()
3505 invert_first_p,invert_second_p,genomecomp,genomebits,genomebits_alt, in worker_setup()
3527 …Cigar_setup(genomecomp,sam_cigar_extended_p,hide_soft_clips_p,merge_samechr_p,md_lowercase_variant… in worker_setup()
3572 if (genomecomp != NULL) { in worker_cleanup()
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| H A D | stage3hr.c | 189 static Genome_T genomecomp; variable
267 genomecomp = genomecomp_in; in Stage3hr_setup()
5585 remap_sequence = Substring_genomic_sequence(&remap_seqlength,substring_other,genomecomp); in Stage3end_new_splice()
5877 remap_sequence = Substring_genomic_sequence(&remap_seqlength,substring_other,genomecomp); in Stage3end_new_distant()
6115 extraleft,extraright,genomecomp); in Stage3end_display_prep()
6164 extraleft,extraright,genomecomp); in Stage3end_display_prep()
6198 extraleft,extraright,genomecomp); in Stage3end_display_prep()
9845 …Substring_print_alignment(fp,pre_junction,substring,post_junction,queryseq,genomecomp,chr,invertp); in print_substrings()
10459 deletion_string = Junction_deletion_string(junction,genomecomp,hit->plusp); in Stage3end_convert_to_pairs_out()
11814 remap_sequence = Stage3end_substrings_genomic_sequence(&remap_seqlength,hit3,genomecomp); in Stage3pair_new()
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| H A D | stage1hr.c | 170 static Genome_T genomecomp; variable
1034 remap_sequence = Stage3end_substrings_genomic_sequence(&remap_seqlength,hit,genomecomp); in remap_to_transcriptome()
3066 genomecomp = genomecomp_in; in Stage1hr_setup()
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| H A D | kmer-search.c | 5180 Genome_T genomecomp,
5194 transcriptome,genomecomp)) != NULL) {
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| /dports/biology/gmap/gmap-2020-09-12/tests/ |
| H A D | Makefile.am | 5 setup.genomecomp.ok setup.ref123positions.ok \
36 mv -f chr17test.genomecomp setup.genomecomp.ok
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| H A D | setup1.test.in | 22 if diff ./chr17test/chr17test.genomecomp ${srcdir}/setup.genomecomp.ok; then
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| H A D | Makefile.in | 458 setup.genomecomp.ok setup.ref123positions.ok \
839 mv -f chr17test.genomecomp setup.genomecomp.ok
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 713 * gmapindex.c: Added code for concatenating genomecomp
1206 * setup.genomecomp.ok: Revised gold standard for extra bytes at end
1348 * genome-write.c: Adding 2 words to the end of genomecomp, needed for
5160 * src, gmapindex.c: Allowing genomecomp to be a command-line argument.
5164 * util, gmap_build.pl.in: Providing genomecomp file as a command-line
8787 branches/2013-07-05-new-genomecomp to implement 32-bit unshuffled
14009 iit_get.out.ok, iittest.iit.ok, map.test.ok, setup.genomecomp.ok,
18487 * snpindex.c: Changed name of SNP genome file from genome to genomecomp.
24956 coords1.test.ok, map.test.in, map.test.ok, setup.genomecomp.ok,
26599 idxoffsets and idxpositions from genomecomp, but has problems.
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