[BioC] MEDIPS, GRanges, IRanges error processing BAM file

[Jonathan Ellis]

Dear Lukas and list,

I'm trying to process a set of BAM files using the latest version of
MEDIPS (1.10.0), but have run into problems creating MEDIPSset objects
for some BAM file.  The following is an example, but I'm getting the
same error for 4 out of 20 BAM files.

> mset <- MEDIPS.createSet("0139202.fq.sam.noDUP.bam.qf.bam", 
+     BSgenome = "Hsapiens", sample_name = "0139202")                                                           
Reading bam alignment 0139202.fq.sam.noDUP.bam.qf.bam 
Total number of imported short reads: 13813686
Creating GRange Object...
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 11345799: range cannot be determined from the supplied arguments 
  (too many NAs)

The data are single-end reads that were aligned with bwa version
0.5.9-r16 (the alignments were done some time ago hence the older
version of bwa), and the corresponding line from the BAM (11,345,799)
is:

19441177        16      chr17   38161416        18      49M     *       0       0       TAGAGTCCGGCGTTCAGGGGCAGGAAGCATCCAGCACGGGAGAAAGATG       BBBBBBBBBBBBBBBBBd_IIX[ffgb[[YJb^d^[[ggee^^cc^^^_      X0:i:1  X1:i:3  XA:Z:chr1,+56337006,49M,3;chr12,-55896993,49M,3;chr4,-22778322,49M,3;   MD:Z:8A7A32     XG:i:0  NM:i:2  XM:i:2  XO:i:0XT:A:U

I'm unsure whether this is a problem with the MEDIPS package or
something from GRanges/IRanges.  As far as I understand the .Call2
function is part of IRanges, but I assume it's failing due to something
passed by MEDIPS.  Any advice or pointers would be greatly appreciated.

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 MEDIPS_1.10.0                     
 [3] DNAcopy_1.34.0                     BSgenome_1.28.0                   
 [5] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.4                
 [7] Biostrings_2.28.0                  GenomicFeatures_1.12.3            
 [9] AnnotationDbi_1.22.6               Biobase_2.20.1                    
[11] GenomicRanges_1.12.4               IRanges_1.18.2                    
[13] BiocGenerics_0.6.0                 BiocInstaller_1.10.3              

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0   bitops_1.0-5     DBI_0.2-7        gtools_3.0.0    
 [5] RCurl_1.95-4.1   Rsamtools_1.12.3 RSQLite_0.11.4   stats4_3.0.1    
 [9] tools_3.0.1      XML_3.98-1.1     zlibbioc_1.6.0