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BIOLIBC(3) Library Functions Manual BIOLIBC(3) NAME BIOLIBC - Library of high-performance low-level functions for bioinfor- matics programming SYNOPSIS One of more of the following headers will be needed for each function used: #include <biolibc/bed.h> #include <biolibc/biolibc.h> #include <biolibc/biostring.h> #include <biolibc/gff.h> #include <biolibc/overlap.h> #include <biolibc/pos-list.h> #include <biolibc/sam.h> #include <biolibc/sam-buff.h> #include <biolibc/vcf.h> cc -I<prefix>/include program.c -L<prefix>/lib -lbiolibc -lxtend PURPOSE Biolibc is a library of fast, memory-efficient, low-level functions for processing biological data. Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications. These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc. Documentation on individual functions should be available soon. FUNCTIONS bl_align_map_seq_exact(3) - Locate little sequence within big sequence bl_align_map_seq_sub(3) - Locate little sequence within big sequence bl_bed_check_order(3) - Compare positions of two bed records bl_bed_gff3_cmp(3) - Compare positions of BED and GFF3 objects bl_bed_read(3) - Read a BED record bl_bed_skip_header(3) - Read past BED header bl_bed_write(3) - Write a BED record bl_chrom_name_cmp(3) - Compare chromosome names numerically or lexically bl_fasta_free(3) - Free memory for a FASTA object bl_fasta_init(3) - Initialize all fields of a FASTA object bl_fasta_read(3) - Read a FASTA record bl_fasta_write(3) - Write a FASTA object bl_fastq_3p_trim(3) - Trim 3' end of a FASTQ object bl_fastq_find_3p_low_qual(3) - Find start of low-quality 3' end bl_fastq_free(3) - Free memory for a FASTQ object bl_fastq_init(3) - Initialize all fields in a FASTQ object bl_fastq_name_cmp(3) - Compare read names of two FASTQ objects bl_fastq_read(3) - Read a FASTQ record bl_fastq_write(3) - Write a FASTQ record bl_fastx_desc(3) - Return description of a FASTX (FASTA or FASTQ) object bl_fastx_desc_len(3) - Return length of a FASTX (FASTA or FASTQ) bl_fastx_free(3) - Free memory for a FASTX (FASTA or FASTQ) object bl_fastx_init(3) - Initialize a FASTX (FASTA or FASTQ) object bl_fastx_plus(3) - Return '+' line of a FASTQ object, NULL if FASTA bl_fastx_plus_len(3) - Return length of FASTQ '+' line, 0 if FASTA bl_fastx_qual(3) - Return FASTQ quality line, NULL if FASTA bl_fastx_qual_len(3) - Return length of FASTQ quality line, 0 if FASTA bl_fastx_read(3) - Read FASTA or FASTQ record bl_fastx_seq(3) - Return sequence of a FASTX (FASTA or FASTQ) object bl_fastx_seq_len(3) - Return sequence length of a FASTX (FASTA or FASTQ) bl_fastx_write(3) - Write FASTA or FASTQ record bl_gff3_copy(3) - Copy a GFF3 object bl_gff3_copy_header(3) - Read and copy a GFF3 header bl_gff3_dup(3) - Duplicate a GFF3 object bl_gff3_extract_attribute(3) - Extract GFF3 attribute by name bl_gff3_free(3) - Free memory for a GFF3 object bl_gff3_index_add(3) - Add a GFF3 feature to an in-memory index bl_gff3_index_seek_reverse(3) - Search backward through GFF3 index bl_gff3_init(3) - Initialize all fields in a GFF3 object bl_gff3_read(3) - Read a GFF3 feature bl_gff3_sam_cmp(3) - Compare positions of a SAM alignment and GFF3 bl_gff3_sam_overlap(3) - Compute overlap between a SAM alignment and a GFF3 feature bl_gff3_skip_header(3) - Read past header in a GFF3 file bl_gff3_to_bed(3) - Convert a GFF3 featuer to a BED object bl_gff3_write(3) - Write a GFF3 feature bl_next_start_codon(3) - Find next start codon bl_next_stop_codon(3) - Find next stop codon bl_overlap_print(3) - Print overlap summary for two features bl_overlap_set_all(3) - Set overlap fields for two features bl_pos_list_add_position(3) - Add a position to a list bl_pos_list_allocate(3) - Initialize position list object bl_pos_list_free(3) - Free a position list object bl_pos_list_from_csv(3) - Convert from comma-separated data to bl_pos_list_sort(3) - Sort a position list bl_sam_buff_add_alignment(3) - Add alignment to SAM buffer bl_sam_buff_alignment_ok(3) - Verify alignment quality bl_sam_buff_check_order(3) - Check sort order of SAM records bl_sam_buff_free_alignment(3) - Free an alignment in a SAM buffer bl_sam_buff_init(3) - Initialize a SAM buffer object bl_sam_buff_out_of_order(3) - Print sort order message and exit bl_sam_buff_shift(3) - Close gap after removing a SAM alignment bl_sam_copy(3) - Copy a SAM object bl_sam_copy_header(3) - Copy SAM header to another stream bl_sam_fclose(3) - Close a stream opened by bl_sam_fopen(3) bl_sam_fopen(3) - Open a SAM/BAM/CRAM file bl_sam_free(3) - Destroy a SAM object bl_sam_gff3_cmp(3) - Compare positions of SAM and GFF3 records bl_sam_gff3_overlap(3) - Return the amount of overlap between a SAM alignment and a GFF3 feature bl_sam_init(3) - Initialize all fields of a SAM object bl_sam_read(3) - Read one SAM record bl_sam_skip_header(3) - Read past SAM header bl_sam_write(3) - Write a SAM object to a file stream bl_vcf_call_downstream_of_alignment(3) - Return true if the location of a VCF call is downstream of an alignment bl_vcf_call_in_alignment(3) - Return true if location of VCF call is bl_vcf_call_out_of_order(3) - Terminate with VCF sort error message bl_vcf_free(3) - Destroy a VCF object bl_vcf_get_sample_ids(3) - Extract sample IDs from a VCF header bl_vcf_init(3) - Initialize fields in a VCF object bl_vcf_parse_field_spec(3) - Convert comma-separated fields to bitmask bl_vcf_read_ss_call(3) - Read a single-sample VCF call bl_vcf_read_static_fields(3) - Read static VCF fields bl_vcf_skip_header(3) - Read past VCF header bl_vcf_skip_meta_data(3) - Read past VCF metadata bl_vcf_write_ss_call(3) - Write a single-sample VCF call bl_vcf_write_static_fields(3) - Write VCF static fields SEE ALSO vcf-split, ad2vcf, vcf2hap, peak-classifier BUGS Please report bugs to the author and send patches in unified diff for- mat. (man diff for more information) AUTHOR J. Bacon BIOLIBC(3)
NAME | SYNOPSIS | PURPOSE | FUNCTIONS | SEE ALSO | BUGS | AUTHOR
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