Strange behaviour with mmfile

bioinfornatics bioinfornatics at fedoraproject.org
Mon Jan 28 16:45:17 PST 2013


Dear,

Why when i try to read this file:

------------Input file-------------------------
$ cat little.fastq 
@H8:C16L5ACXX:8:1101:1168:2103/1
TCTGAAGGCATGCTGCAATTGTGAATGGCAGAAATGT
+
?@@DD>DBDAFDF at 4CFGICFHHECHEEBF;E at FFFG
@H8:C16L5ACXX:8:1101:1223:2104/1
CTCACTTTTGTACTTTAGACAAGCGCTTTTAGTAGTGCT
+
@@;DD;?DHFFHFG9FAFCEGFGBFE1EFFGFGGHG9D*
@H8:C16L5ACXX:8:1101:1166:2142/1
ATCTGGGAAGACGCCGCCGGGTTCAAATCACCTTGGTCGGCATCGTCGATCCGC
+
;=?DDDDD3C??)@:E1CDD)?B?B<99BB8=<8)8.=A88<8)56;9/>2=??


By using mmfile ubyte given do not corresponding to the letter.
By example for @ i expect 64 but i got 127


---------------Result-----------------------
$ ./test_mmap little2.fastq
127 
69 E
76 L
70 F
2 
1 
1 
0 
0 
0 
0 
0 
0 
0 
0 
0 
2 
0 
62 >
0 
… and that continue

Big thanks

Note i have try with both ldc and gdc



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