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pairtobed dies on RNA-seq bam #157

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

1. BAM file contains RNA-seq reads aligned to the genome using MapSplice
2. BAM file was sorted by query name using samtools sort
3. Tried to extract all read pairs that overlap a particular region of interest 
with the following command:
bedtools pairtobed -abam name.sorted.bam -b region.bed

What is the expected output? What do you see instead?

No output produced except the following error message immediately after the 
command was issued:

terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check
Abort

What version of the product are you using? On what operating system?

bedtools v2.17.0 on CentOS release 5.4 

Please provide any additional information below.

Original issue reported on code.google.com by wangz...@gmail.com on 1 Aug 2013 at 4:57