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#92 tg_index -C -> gap5 drops quality values past read pos 25

closed
Gap5 (15)
5
2011-07-28
2011-07-11
No

Hi James,

assuming one has a file "bla.caf" and does the following:

tg_index -C bla.caf
gap5 bla.0.g5d
In gap5: File -> Export sequences -> as CAF

then all the reads in the resulting "bla.0.caf" file will have only the first 25 quality values set and the remaining qualities afre 0 like in the example:

BaseQuality : somedata_8_44_5274_52813#TGAAAA/1.10246
38 38 38 38 38 38 38 38 38 38 38 38 38 36 36 31 38 38 36 38 38
38 37 31 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Looking at the gap5 display tells me that already in gap5 things do not look as they should.

Best,
Bastien

Discussion

  • Andrew Whitwham

    Andrew Whitwham - 2011-07-12

    Hi Bastien,

    I can't replicate this. I imported a 250Mb caf file then exported it as caf and it looked fine, all qualities intact. I then re-imported that caf file and exported it again. Still no loss of qualities on the reads.

    Is there anything odd about the layout of your caf file?

    I'm using the latest code from SVN.

    Andrew

     
  • Bastien Chevreux

    Hello Andrew,

    sorry for the long delay, I was on a conference and then it took a while before I found out how to reproduce reliably.

    I'll change the summary to: tg_index has the problems (described earlier) with CAF files generated by gap2caf.

    I'll attach an archive with demo data to reproduce. Note that "demo2_out.caf" is the original CAF file written by MIRA (which converts nicely to gap5 btw):
    1) caf2gap -project demo2 -ace demo2_out.caf
    2) gap2caf -project DEMO2 >demo2_fromgap4.caf
    3) tg_index -C demo2_fromgap4.caf
    4) gap5 demo2_fromgap4.0 -> File -> Export Sequences -> Format CAF -> OK
    5) less demo2_fromgap4.0.caf

     
  • Bastien Chevreux

    Example files to reproduce bug

     
  • Andrew Whitwham

    Andrew Whitwham - 2011-07-21

    Thanks Bastien,

    I can reproduce it now.

    Andrew

     
  • Andrew Whitwham

    Andrew Whitwham - 2011-07-21

    Okay, the demo2_fromgap4.caf file had spaces at the beginning of some lines within the quality values block. tg_index was treating that as the end of the quality values.

    Parsing error, should be fixed now.

    Andrew

     
  • Andrew Whitwham

    Andrew Whitwham - 2011-07-28
    • assigned_to: jkbonfield --> awhitwham
    • status: open --> closed
     

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