[Bioc-sig-seq] ShortRead qa() no longer working

[Dario Strbenac]

Hello again,

Both of those checks worked out, and I still get the error :

> fl = list.files(path, "fastq.gz", full=TRUE)
> fl
[1] "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1/s_1_sequence.fastq.gz"
> 
> 
> .Call(ShortRead:::.read_solexa_fastq, fl, TRUE)
$sread
  A DNAStringSet instance of length 27278762
           width seq
       [1]    36 TTCAATGATTCCATTTGATTCCATNNGNNNNNNNNT
       [2]    36 TGGAATCGTCATCGAATGAATTGANNGNNNNNNNNG
       [3]    36 TATAAAAACTAGACGGAGTCATTCNNANNNNNNNNT
       [4]    36 GCAAAGCTCTTTTCCGTTTGACTCNNGNNNNNNNNA
       [5]    36 TGTTGATTCCATTCGATTCCATTCNNTNANNNNNNC
       [6]    36 GGAGTTCGAGACTGGCCTGGCCAANATNGNNNNNNC
       [7]    36 GAACAGTTTCATCACATGTAGTAAGCANAGNNNNNG
       [8]    36 TGACTCCTTTCATTTCCATTCGATNATNANNNNNNT
       [9]    36 TAAGGAGGATTTTAGGTATGGGTTTTTCATANNTGC
       ...   ... ...
[27278754]    36 GAACCTGAGAGGCGGAGGTTGCGGTGNGCAAAGAGT
[27278755]    36 TGGAATCTAATGGAATAATTGAACAGNAATGAATGG
[27278756]    36 GGAATCAATATCAAACGGAAAAAAACNGAATTATCG
[27278757]    36 TGGAAATGAATGGAATCATCATCGAANGGAATCGAA
[27278758]    36 NATCACTCCCGGCTAACTTTTCATATNTTTTGTAGA
[27278759]    36 NCATGCTGAGAAAGTTCTTCATGACGNATGCATTTA
[27278760]    36 NAATGGACTCAAATGGAATTATCCTCNAATGGAATC
[27278761]    36 NAGAAAAGGAAATATCTTCGTATAAANACTAGACAG
[27278762]    36 NTATCGAATGGAATCGAAGAGAATCANCGAATGGCC

$id
  A BStringSet instance of length 27278762
           width seq
       [1]    22 GAPC:1:1:1142:2476#0/1
       [2]    23 GAPC:1:1:1142:10510#0/1
       [3]    23 GAPC:1:1:1143:16066#0/1
       [4]    23 GAPC:1:1:1144:20655#0/1
       [5]    23 GAPC:1:1:1144:15460#0/1
       [6]    22 GAPC:1:1:1145:9727#0/1
       [7]    22 GAPC:1:1:1145:4010#0/1
       [8]    23 GAPC:1:1:1145:21159#0/1
       [9]    22 GAPC:1:1:1147:6527#0/1
       ...   ... ...
[27278754]    25 GAPC:1:120:19834:3792#0/1
[27278755]    26 GAPC:1:120:19836:10159#0/1
[27278756]    26 GAPC:1:120:19838:12475#0/1
[27278757]    25 GAPC:1:120:19840:4819#0/1
[27278758]    26 GAPC:1:120:19844:11082#0/1
[27278759]    25 GAPC:1:120:19848:9908#0/1
[27278760]    25 GAPC:1:120:19854:3323#0/1
[27278761]    26 GAPC:1:120:19856:17724#0/1
[27278762]    25 GAPC:1:120:19864:9093#0/1

$quality
  A BStringSet instance of length 27278762
           width seq
       [1]    36 babbbbbbbbbbbbbbb`bbBBBBBBBBBBBBBBBB
       [2]    36 bbbbbbbbbbbbbbb\bb^^BBBBBBBBBBBBBBBB
       [3]    36 a_aa\ab]]aabbbbbbb_bBBBBBBBBBBBBBBBB
       [4]    36 bYbb\bbbbbbbb^`^XZ]^BBBBBBBBBBBBBBBB
       [5]    36 ___[_YU^Y^^^^aaT^W^^BBBBBBBBBBBBBBBB
       [6]    36 OOONNOOOON\bb_bbbbbBBBBBBBBBBBBBBBBB
       [7]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
       [8]    36 ^bY_bb_bb]^b_bbbb\b^BBBBBBBBBBBBBBBB
       [9]    36 OOOOLOGNNO]]SZ]`TW^`]XU]]a`aa`BBBBBB
       ...   ... ...
[27278754]    36 ]Z]]]Q___[UWWWZ]^`O^BBBBBBBBBBBBBBBB
[27278755]    36 b`bb`bbbca````_bbba`[a_a`[B^[^^^Z^^`
[27278756]    36 `bbbbb`_bZ\X\Z\a_aBBBBBBBBBBBBBBBBBB
[27278757]    36 bbbbb__a___aa_aabbab_bbbbBBBBBBBBBBB
[27278758]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
[27278759]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
[27278760]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
[27278761]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
[27278762]    36 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

> 
> QAfastq <- qa(path, "fastq.gz", "fastq")
Error in stop(msg, " ", errors, domain = NA) : 
  no function to return from, jumping to top level
Error in slot(object, ".srlist") : 
  cannot get a slot (".srlist") from an object of type "NULL"
In addition: Warning message:
UnspecifiedWarning
  elements: 1
  UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
 error in evaluating the argument 'dirPath' in selecting a method for function 'qa'