[BioC] Rsamtools yieldTabix Skips Comment Lines

[Martin Morgan]

Hi Dario --

On 06/04/2012 12:00 AM, Dario Strbenac wrote:
> Hello,
>
> In a previous version, I was able to read a tabix file, including the first line that started with # and had column names. Now with Rsamtools 1.8.4, it skips that line and the first element of the character vector is the first record of the tabix file. Any way to get the old behaviour back so that I can know the column names ?
>
> anno<- "http://genomesavant.com/savant/data/hg18/hg18.refGene.gz"
> txTabix<- TabixFile(anno)
> txStrings<- yieldTabix(txTabix, yieldSize = 100000)
> close(txTabix)
> txStrings[[1]] # Not the row of column names any longer.

 > tail(headerTabix(txTabix)$header, 1)
[1] 
"#bin\tname\tchrom\tstrand\ttxStart\ttxEnd\tcdsStart\tcdsEnd\texonCount\texonStarts\texonEnds\tscore\tname2\tcdsStartStat\tcdsEndStat\texonFrames"


>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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