#346 Colorspace Error

[Stephen K]

Hi, This is my first time using bowtie to align colorspace reads so I'm not 100% sure I'm doing everything correctly but I keep running into this error:

/usr/include/seqan/sequence/string_base.h:237 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 40 >= 40 (Trying to access an element behind the last one!)
Aborted (core dumped)

Bowtie version is 1.0.0 and the command I'm using is:
bowtie -C -p 6 ./mm10/Sequence/BowtieIndexColorspace/mm10_col -q ./Rpf_control/test.fastq --un ./test.sam

The majority of the reads in the fastq file seem to process fine but some will result in the error above. One such read is:

@SRR1964308.1143 1_217_1807 length=50
T031201023301211101303022322232303211313030
+SRR1964308.1143 1_217_1807 length=50
!@@@=@@@@//@666@?@<=6@*@2@@2@@@8<82@?6<=/6/

If I change the last symbol of the quality line from "/" to "@" the read is then processed without error.