generating tdf file from BAM

[Morioka MS]

Hi,

Im trying to make tdf file, using (sorted) BAM file.
When I use SAM file (source file of BAM file), igvtools sucessfully
generate tdf file.
But in case of bam file I can not.
Igvtools tells me "no features were found" in described below.
Any suggestion why this happens?

Thanks,

Masaki Suimye Morioka

IGVtools ver.: im sorry i can not find out version of Igvtools


-bash-3.2$ igvtools count test.sort.bam test.tdf mm9

###########################################################
Computing coverage. File = test.bam
Window size = 25
Ext factor = 0
java.lang.RuntimeException: Invalid file pointer: 890
at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:159)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:217)
at
org.broad.igv.sam.reader.BAMQueryReader.iterator(BAMQueryReader.java:
78)
at org.broad.igv.tools.CoverageCounter.parse(CoverageCounter.java:
120)
at org.broad.igv.tools.Preprocessor.count(Preprocessor.java:776)
at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:243)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:153)
Caused by: java.io.IOException: Invalid file pointer: 890
at
net.sf.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:
205)
at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:157)
... 6 more
No features were found that matched chromosomes in genome: mm9
100.0%
###########################################################

[Jim Robinson]

Hi Masaki,

The error indicates that either your BAM file is corrupt, or you are
possibly using an old version of IGVTools. Could you try downloading
the latest version at http://www.broadinstitute.org/igvdata/downloads/igvtools_1.5.15.zip?
If you still have the problem with this version then please let us
know how the BAM file was created (with which package and version).

-- Jim

[Masaki MS]

Hi Jim,

Thanks so much! 

I can successfully convert BAM to tdf by latest ver. of Igvtool.

Masaki.

2011/6/15 Jim Robinson <jrob...@broadinstitute.org>