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bl_align_map_seq_exact(3)   Library Functions Manual   bl_align_map_seq_exact(3)

NAME
     bl_align_map_seq_exact() - Locate little sequence in big sequence

LIBRARY
     #include <biolibc/align.h>
     -lbiolibc -lxtend

SYNOPSIS
     size_t  bl_align_map_seq_exact(const bl_align_t *params,
     const char *big, size_t big_len,
     const char *little, size_t little_len)

ARGUMENTS
     params	 bl_align_t parameters.  Only min_match is used.
     big	 Sequence to be searched for matches to little
     little	 Sequence to be located within big

DESCRIPTION
     Locate the leftmost (farthest 5') match for sequence little within sequence
     big, using exact matching only.

     The content of little is assumed to be all upper case.  This improves speed
     by  avoiding  numerous  redundant toupper() conversions on the same string,
     assuming multiple big strings will be searched for little,  as  in  adapter
     removal  and  read mapping.  Use strlupper(3) or strupper(3) before calling
     this function if necessary.

     A minimum of min_match bases must	match  between	little	and  big.   This
     mainly  matters  near  the end of big, where remaining bases are fewer than
     the length of little.

     Note that alignment is not an exact science.  We cannot detect  every  true
     little  sequence without falsely detecting other sequences, since it is im-
     possible to know whether any given sequence is really from  the  source  of
     interest (e.g. an adapter) or naturally occurring from another source.  The
     best  we  can  do	is  guestimate what will provide the most true positives
     (best statistical power) and fewest false positives.

     In the case of adapter removal, it is also not usually important to  remove
     every  adapter,  but  only  to  minimize adapter contamination.  Failing to
     align a small percentage of sequences due to adapter contamination will not
     change the story told by the downstream  analysis.   Nor  will  erroneously
     trimming  off  the 3' end of a small percentage of reads containing natural
     sequences resembling adapters.  Just trimming exact matches of the  adapter
     sequence will generally remove 99% or more of the adapter contamination and
     minimize  false-positives.  Tolerating 1 or 2 differences has been shown to
     do slightly better overall.  Modern read mapping software is also	tolerant
     of adapter contamination and can clip adapters as needed.

RETURN VALUES
     Index  of	little sequence within big if found, index of null terminator of
     big otherwise

EXAMPLES
     bl_param_t  params;
     bl_fastq_t  read;
     char	 *adapter;
     size_t	 index;

     bl_align_set_min_match(&params, 3);
     index = bl_align_map_seq_exact(&params,
	 BL_FASTQ_SEQ(&read), BL_FASTQ_SEQ_LEN(&read),
	 little, strlen(adapter)3, 10);
     if ( index != BL_FASTQ_SEQ_LEN(&read) )
	 bl_fastq_3p_trim(&read, index);

SEE ALSO
     bl_align_map_seq_sub(3), bl_align_set_min_match(3), bl_fastq_3p_trim(3)

						       bl_align_map_seq_exact(3)
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