ERROR: Unknown combination found when converting to basespace: [Y] & [T]

[GoogleCodeExporter]

What steps will reproduce the problem?
1. I'm trying to align Solid PE 50/35bp to hg19 masked with snp132
2.
3.

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

------------------------------------------------------------------------------
MosaikAligner 1.0.1388                                              2010-02-01
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
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- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 10
- Using a hash size of 15
- Aligning in colorspace (SOLiD)
- Using 8 processors
- Using a Smith-Waterman bandwidth of 21
- Using an alignment candidate threshold of 27bp.
- Setting hash position threshold to 100
- Using a jump database for hashing. Storing keys & positions in memory.
- loading basespace reference sequences... finished.
- loading jump keys database into memory... finished.
- loading jump positions database into memory... finished.
- loading reference sequence... finished.

Aligning read library (42214716):
 0% [                                              ]                                  |ERROR: Unknown combination found when converting to basespace: [Y] & [T]

What version of the product are you using? On what operating system?
MosaikAligner 1.0.1388, Linux Mint

Please provide any additional information below.

Original issue reported on code.google.com by tremblay...@gmail.com on 27 Apr 2011 at 1:35

[GoogleCodeExporter]

Also, when I'm using an unmasked reference ... I get a segmentation fault. 

Original comment by tremblay...@gmail.com on 27 Apr 2011 at 2:03

[GoogleCodeExporter]

did you get to the bottom of this error? I have just come across the same one

MosaikAligner 1.1.0021                                              2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 4
- Using a hash size of 10
- Aligning in colorspace (SOLiD)
- Using 8 processors
- Using a jump database for hashing. Storing keys & positions in memory.
- Reporting all unaligned reads to unaligned_reads.fastq.
- loading basespace reference sequences... finished.
- loading reference sequence... finished.
- loading jump key database into memory... finished.
- loading jump positions database into memory... finished.

Aligning read library (105541755):
 0% [                                    ]                                  /ERROR: Unknown combination found when converting to basespace: [Y] & [T]

Original comment by cboust...@gmail.com on 16 Aug 2011 at 5:55