dear all:
       sorry to disturb you ,especially martin.
but i feel so confused, when i use
alnRanges <- readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM")
it wored well
but when i use
paraFlag <- scanBamFlag(hasUnmappedMate = T)
para <-ScanBamParam(flag = paraFlag)
alnRanges <-
readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM",which=para)

it reported error

Error in open.BamFile(BamFile(file, index), "rb") :
  failed to load BAM index
  file: /home/sgao/Algae_data/s_5_1-IS_sequence.bam
In addition: Warning message:
In open.BamFile(BamFile(file, index), "rb") :
  [bam_index_load] fail to load BAM index.



> sessionInfo()
R version 2.13.2 (2011-09-30)
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=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] ShortRead_1.10.4    Rsamtools_1.4.3     lattice_0.19-33
[4] Biostrings_2.20.4   GenomicRanges_1.4.8 IRanges_1.10.6
loaded via a namespace (and not attached):
[1] Biobase_2.12.2 grid_2.13.2    hwriter_1.3

	[[alternative HTML version deleted]]

