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Searched refs:SUBREADputs (Results 1 – 25 of 27) sorted by relevance

12

/dports/biology/subread/subread-2.0.2-source/src/
H A Dcore-interface-aligner.c82 SUBREADputs(""); in print_usage_core_aligner()
84 SUBREADputs(""); in print_usage_core_aligner()
88 SUBREADputs(""); in print_usage_core_aligner()
106 SUBREADputs(""); in print_usage_core_aligner()
109 SUBREADputs(""); in print_usage_core_aligner()
111 SUBREADputs(""); in print_usage_core_aligner()
113 SUBREADputs(""); in print_usage_core_aligner()
115 SUBREADputs(""); in print_usage_core_aligner()
117 SUBREADputs(""); in print_usage_core_aligner()
120 SUBREADputs(""); in print_usage_core_aligner()
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H A Dcore-interface-subjunc.c82 SUBREADputs(""); in print_usage_core_subjunc()
84 SUBREADputs(""); in print_usage_core_subjunc()
86 SUBREADputs(""); in print_usage_core_subjunc()
88 SUBREADputs(""); in print_usage_core_subjunc()
95 SUBREADputs(""); in print_usage_core_subjunc()
102 SUBREADputs(""); in print_usage_core_subjunc()
105 SUBREADputs(""); in print_usage_core_subjunc()
107 SUBREADputs(""); in print_usage_core_subjunc()
109 SUBREADputs(""); in print_usage_core_subjunc()
111 SUBREADputs(""); in print_usage_core_subjunc()
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H A Dread-repair.c18 SUBREADputs(""); in print_usage_pairer()
20 SUBREADputs(""); in print_usage_pairer()
22 SUBREADputs(""); in print_usage_pairer()
24 SUBREADputs(""); in print_usage_pairer()
26 SUBREADputs(""); in print_usage_pairer()
28 SUBREADputs(""); in print_usage_pairer()
30 SUBREADputs(""); in print_usage_pairer()
32 SUBREADputs(""); in print_usage_pairer()
36 SUBREADputs(""); in print_usage_pairer()
38 SUBREADputs(""); in print_usage_pairer()
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H A Dfullscan.c40 SUBREADputs("a specified read."); in fullscan_usage()
41 SUBREADputs(""); in fullscan_usage()
42 SUBREADputs("Usage:"); in fullscan_usage()
43 SUBREADputs(""); in fullscan_usage()
45 SUBREADputs(""); in fullscan_usage()
46 SUBREADputs("Required arguments:"); in fullscan_usage()
47 SUBREADputs(""); in fullscan_usage()
49 SUBREADputs(""); in fullscan_usage()
51 SUBREADputs(""); in fullscan_usage()
53 SUBREADputs(""); in fullscan_usage()
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H A DqualityScores.c463 SUBREADputs(""); in qualscore_usage()
465 SUBREADputs(""); in qualscore_usage()
467 SUBREADputs(""); in qualscore_usage()
470 SUBREADputs(""); in qualscore_usage()
473 SUBREADputs(""); in qualscore_usage()
475 SUBREADputs(""); in qualscore_usage()
477 SUBREADputs(""); in qualscore_usage()
479 SUBREADputs(""); in qualscore_usage()
481 SUBREADputs(""); in qualscore_usage()
484 SUBREADputs(""); in qualscore_usage()
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H A DflattenAnnotations.c76 SUBREADputs(""); in flatAnno_print_usage()
77 SUBREADputs("Usage:"); in flatAnno_print_usage()
79 SUBREADputs(""); in flatAnno_print_usage()
81 SUBREADputs(""); in flatAnno_print_usage()
83 SUBREADputs(""); in flatAnno_print_usage()
85 SUBREADputs(""); in flatAnno_print_usage()
87 SUBREADputs(""); in flatAnno_print_usage()
91 SUBREADputs(""); in flatAnno_print_usage()
95 SUBREADputs(""); in flatAnno_print_usage()
98 SUBREADputs(""); in flatAnno_print_usage()
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H A Dcoverage_calc.c42 SUBREADputs(""); in calcCount_usage()
43 SUBREADputs("Usage"); in calcCount_usage()
44 SUBREADputs(""); in calcCount_usage()
46 SUBREADputs(""); in calcCount_usage()
47 SUBREADputs("Required arguments:"); in calcCount_usage()
48 SUBREADputs(""); in calcCount_usage()
50 SUBREADputs(""); in calcCount_usage()
53 SUBREADputs(""); in calcCount_usage()
55 SUBREADputs(""); in calcCount_usage()
57 SUBREADputs(""); in calcCount_usage()
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H A DremoveDupReads.c298 SUBREADputs(""); in print_usage_rrr()
299 SUBREADputs("Usage:"); in print_usage_rrr()
301 SUBREADputs("Required arguments:"); in print_usage_rrr()
302 SUBREADputs(""); in print_usage_rrr()
304 SUBREADputs(""); in print_usage_rrr()
307 SUBREADputs(""); in print_usage_rrr()
308 SUBREADputs("Optional arguments:"); in print_usage_rrr()
309 SUBREADputs(""); in print_usage_rrr()
311 SUBREADputs(""); in print_usage_rrr()
315 SUBREADputs(""); in print_usage_rrr()
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H A Dpropmapped.c195 SUBREADputs(""); in propMapped_usage()
197 SUBREADputs(""); in propMapped_usage()
198 SUBREADputs("Usage:"); in propMapped_usage()
199 SUBREADputs(""); in propMapped_usage()
201 SUBREADputs(""); in propMapped_usage()
203 SUBREADputs(""); in propMapped_usage()
206 SUBREADputs(""); in propMapped_usage()
208 SUBREADputs(""); in propMapped_usage()
210 SUBREADputs(""); in propMapped_usage()
214 SUBREADputs(""); in propMapped_usage()
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H A Dgen_rand_reads.c39 SUBREADputs(""); in print_usage_gen_reads()
41 SUBREADputs(""); in print_usage_gen_reads()
45 SUBREADputs(""); in print_usage_gen_reads()
49 SUBREADputs(""); in print_usage_gen_reads()
51 SUBREADputs(""); in print_usage_gen_reads()
53 SUBREADputs(""); in print_usage_gen_reads()
55 SUBREADputs(""); in print_usage_gen_reads()
57 SUBREADputs(""); in print_usage_gen_reads()
60 SUBREADputs(""); in print_usage_gen_reads()
62 SUBREADputs(""); in print_usage_gen_reads()
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H A DSNPCalling.c1513 SUBREADputs(""); in print_usage_snp()
1515 SUBREADputs(""); in print_usage_snp()
1517 SUBREADputs(""); in print_usage_snp()
1521 SUBREADputs(""); in print_usage_snp()
1524 SUBREADputs(""); in print_usage_snp()
1527 SUBREADputs(""); in print_usage_snp()
1529 SUBREADputs(""); in print_usage_snp()
1535 SUBREADputs(""); in print_usage_snp()
1537 SUBREADputs(""); in print_usage_snp()
1542 SUBREADputs(""); in print_usage_snp()
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H A Dindex-builder.c1109 SUBREADputs(""); in main()
1112 SUBREADputs(""); in main()
1114 SUBREADputs(""); in main()
1116 SUBREADputs(""); in main()
1118 SUBREADputs(""); in main()
1123 SUBREADputs(""); in main()
1129 SUBREADputs(""); in main()
1131 SUBREADputs(""); in main()
1160 SUBREADputs(""); in main()
1214 SUBREADputs(""); in main()
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H A DmergeVCF.c340 SUBREADputs(""); in common_var_usage()
342 SUBREADputs(" and/or SNPs."); in common_var_usage()
343 SUBREADputs(""); in common_var_usage()
345 SUBREADputs(" ExactSNP, subindel and other tools."); in common_var_usage()
346 SUBREADputs(""); in common_var_usage()
347 SUBREADputs("Usage:"); in common_var_usage()
348 SUBREADputs(""); in common_var_usage()
350 SUBREADputs(""); in common_var_usage()
351 SUBREADputs("Required arguments:"); in common_var_usage()
352 SUBREADputs(""); in common_var_usage()
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H A DreadSummary.c682 SUBREADputs(""); in print_FC_configuration()
684 SUBREADputs(""); in print_FC_configuration()
846 SUBREADputs(""); in print_FC_configuration()
867 SUBREADputs(""); in print_FC_results()
870 SUBREADputs(""); in print_FC_results()
7563 SUBREADputs(""); in print_usage()
7568 SUBREADputs(""); in print_usage()
7573 SUBREADputs(""); in print_usage()
7578 SUBREADputs(""); in print_usage()
7582 SUBREADputs(""); in print_usage()
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H A Dsubtools.c24 SUBREADputs("Usage:"); in subtools_usage()
25 SUBREADputs(""); in subtools_usage()
26 …SUBREADputs(" ./subtools -i input_file -o output_file --informat <SAM|BAM> --outformat <SAM|BAM> … in subtools_usage()
27 SUBREADputs(""); in subtools_usage()
H A DSUBindel.c266 SUBREADputs(""); in print_configuration_forindel()
268 SUBREADputs(""); in print_configuration_forindel()
285 SUBREADputs(""); in print_configuration_forindel()
300 SUBREADputs(""); in print_summary()
H A Dglobal-reassembly.c155 SUBREADputs("\nUsage:"); in GRA_print_usage()
226 SUBREADputs(""); in GRA_check_config()
227 SUBREADputs(""); in GRA_check_config()
229 SUBREADputs(""); in GRA_check_config()
235 SUBREADputs("\tFile Format\t:\tFASTQ"); in GRA_check_config()
238 SUBREADputs("\tFile Format\t:\tBAM"); in GRA_check_config()
240 SUBREADputs("\tFile Format\t:\tSAM"); in GRA_check_config()
243 SUBREADputs(""); in GRA_check_config()
801 SUBREADputs("\nThe reassembly index is built.\n"); in GRA_build_read_index()
1486 SUBREADputs(""); in GRA_reassemble_reads_LR()
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H A Dsubread.h138 #define SUBREADputs(x) fprintf(stderr, "%s\n", x) macro
149 #define SUBREADputs(x) msgqu_printf("%s\n",(x)) macro
172 #define fatal_memory_size(a) SUBREADputs(MESSAGE_OUT_OF_MEMORY);
H A Dsorted-hashtable.c100 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_create_ex()
139 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in _gehash_resize_bucket()
180 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in _gehash_resize_bucket()
253 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_insert()
1470 SUBREADputs("ERROR: the index format is unrecognizable."); in gehash_load()
1480 SUBREADputs("Creating buckets."); in gehash_load()
1481 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_load()
1524 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_load()
1579 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_load()
1594 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gehash_load()
H A Dtx-unique.c414 …SUBREADputs("./txUnique -a <GTF_file> -o <output_text> { -g <gene_id_column> -t <transcript_id_col… in txunique_parse_options()
420 SUBREADputs("The GTF file name and the output file name must be specified."); in txunique_parse_options()
440 if(!ret) SUBREADputs("All finished.");
H A Dgene-algorithms.c650 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in init_allvote()
1958 SUBREADputs(""); in dynamic_align()
1981 SUBREADputs(""); in dynamic_align()
1983 SUBREADputs(""); in dynamic_align()
1984 SUBREADputs(""); in dynamic_align()
1990 SUBREADputs(""); in dynamic_align()
2527 SUBREADputs(""); in print_votes()
H A Dgene-value-index.c36 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gvindex_init()
202 SUBREADputs("ERROR: the index is incomplete."); in gvindex_load()
214 SUBREADputs(MESSAGE_OUT_OF_MEMORY); in gvindex_load()
H A Dsambam-file.c66 SUBREADputs("ERROR: BAM format is broken."); in SamBam_fetch_next_chunk()
456 SUBREADputs("ERROR: buffer insufficient"); in PBam_get_next_zchunk()
465 SUBREADputs("ERROR: the input BAM file is broken."); in PBam_get_next_zchunk()
1240 if(!writer -> is_internal_error)SUBREADputs("ERROR: no space left in the output directory."); in SamBam_writer_add_chunk()
H A Dcore.c517 SUBREADputs("show_progress can only be called by thread#0\n"); in show_progress()
815 SUBREADputs("ERROR: the sort by coordinate function only works on 64-bit computers.");
820 SUBREADputs("ERROR: you shouldn't specify keep input order and sort by coordinate at same time.");
825 …if(global_context -> config.is_BAM_output==0)SUBREADputs("ERROR: SAM output doesn't support read s…
826 else SUBREADputs("ERROR: STDOUT output doesn't support read sorting by coordinates.");
950 SUBREADputs("ERROR: the BAM format is broken.");
H A Dcore-indel.c4704 SUBREADputs(""); in core_dynamic_align()
4725 SUBREADputs(""); in core_dynamic_align()
4730 SUBREADputs(""); in core_dynamic_align()
4731 SUBREADputs(""); in core_dynamic_align()
4737 SUBREADputs(""); in core_dynamic_align()

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