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

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\texonCoun t\texonStarts\texonEnds\tscore\tname2\tcdsStartStat\tcdsEndStat\texonF rames" > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793