pezmaster31/bamtools — Issue #33: std::out_of_range() for bamtools convert "pileup" option
Author: arq5x
Created: 2012-02-05 16:35:17+00:00
State: open

Hi Derek,

I've been playing around with the pileup option in bamtools convert. In testing it with a pos-sorted BAM file from the 1000 Genomes project, I found that it exits with a std::out_of_range() error. I tested it with:

1. A remote 1000G file.
2. Downloading the file locally.
3. Downloading the file locally and using a -fasta file.

Below is the log. Any ideas?

bamtools convert -format pileup -in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00739/alignment/HG00739.chrom20.ILLUMINA.bwa.PUR.low_coverage.20111114.bam
20	59993	N	6	^2G^>G^>G^>G^>G^>G	JG>G=I
20	59994	N	6	TTTTTT	EC4@BH
20	59995	N	6	GGGGGG	JGCIDJ
20	59996	N	6	AAAAAA	IEDAAJ
20	59997	N	6	CCCCCC	HFDB>H
20	59998	N	6	TTTTTT	JIHDHK
20	59999	N	6	CCCCCC	IGCFHK
20	60000	N	6	AAAAAA	I8EJHI
20	60001	N	6	GGGGGG	JGDJEI
20	60002	N	6	AAAAAA	HGAIDJ
20	60003	N	6	TTTTTT	HIAHHH
20	60004	N	6	CCCCCC	JHEIDK
20	60005	N	6	CCCCCC	JEEKBK
20	60006	N	6	AAAAAA	GGFECJ
20	60007	N	6	GGGGGG	LHFLEL
20	60008	N	6	AAAAAA	:HFGCJ
20	60009	N	6	GGGGGG	GFHEHL
20	60010	N	6	GGGGGG	GGGFIJ
20	60011	N	6	TTGTTT	K
20	60014	N	6	AAAAAA	GA7A2I
20	60015	N	7	AAAAAA^]A	FECA5L@
20	60016	N	7	GGGGGGG	FDEGALA
20	60017	N	7	AAAAAAA	E7>C;IC
20	60018	N	7	GGGGGGG	GBBFAJG
20	60019	N	7	GGGGGGG	JJAFHKG
20	60020	N	8	AAAAAAA^]A	EH>F@HD<
20	60021	N	8	AAAAAAAA	AFH?6JHC
20	60022	N	8	GGGGGGGG	IIHECJHD
20	60023	N	9	GGGGGGGG^]G	JFHE?HHD<
20	60024	N	9	AAAA$AAAAA	?B;EGGCCB
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::at
Abort trap