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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