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bl_align_map_seq_sub(3)     Library Functions Manual	 bl_align_map_seq_sub(3)

NAME
     bl_align_map_seq_sub() - Locate little sequence in big sequence

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

SYNOPSIS
     size_t  bl_align_map_seq_sub(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 and
     max_mismatch_percent are 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, tolerating the given percentage of mismatched bases.

     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.

     A maximum of max_mismatch_percent mismatched bases are tolerated  to  allow
     for  read errors. This is taken as a percent of little, or the same percent
     of remaining bases in big, whichever is smaller.  Note that the  NUMBER  of
     allowed  mismatched  bases tolerated is truncated from the percent calcula-
     tion.  E.g. using 10% tolerance, 0 mismatched bases are tolerated	among  9
     total bases, or 1 mismatch among 10 total.

     Higher  values  of max_mismatch_percent will results in slightly longer run
     times, more alignments detected,  and  a  higher  risk  of  false-positives
     (falsely identifying other big sequences as matching little.

     Indels (insertions and deletions) are not currently handled.

     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);
     bl_align_set_max_mismatch_percent(&params, 10);
     index = bl_align_map_seq_sub(&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_exact(3), bl_align_set_min_match(3), bl_align_set_max_mis-
     match_percent(3), bl_fastq_3p_trim(3)

							 bl_align_map_seq_sub(3)
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