Re: [maq-help] Question about map default maximum mismatches

[Heng Li <lh...@sa...>]

Hello Royden,

Option '-n' and macro 'MAX_MISMATCH' mean different things. With '-n  
2', seed hits with 2 or fewer mismatches are guaranteed to be found.  
And with 'MAX_MISMATCH=3', maq also finds about 40% of 3-mismatch  
hits, but not all of them. You could find all 3-mismatch hit with '-n  
3', but then maq would be 3 times slower.

Heng


On 30 Apr 2008, at 23:55, Royden Clark wrote:

> The maq pdf that I downloaded with the files stated
> map maq map [!n nmis] [!a maxins] [!c] [!1 len1] [!2 len2] [!d  
> adap3] [!m mutrate] [!u
> dump] [!e maxerr] [!M c!g] [!N] out.aln.map in.ref.bfa in.read1.bfq  
> [in.read2.bfq] 2>
> out.map.log
> Map reads to the reference sequences.
> OPTIONS:
> !n INT Number of maximum mismatches that can always be found [2]
> !a INT Maximum outer distance for a correct read pair [250]
> !c Map reads in the colour space (for SOLiD only)
> !1 INT Read length for the rst read, 0 for auto [0]
> !2 INT Read length for the second
>
> that the default for maximum number of mismatches is 2
>
> but in the code for
>
> match.hh
> #ifdef _FASTMAP
> #  define SEED_LENGTH 28
> #  define MAX_MISMATCH 3
> #else
> #  define SEED_LENGTH 24
> #  define MAX_MISMATCH 4
> #endif
>
>
>
> Is the real default then 3 or 4 instead of 2?
>
> Thank you
> Royden 
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