Regression since b1804d3 (2014-03-27) causes segfault in MosaikAligner

[bede]

@wanpinglee , a segfault-causing bug in MosaikAligner has been introduced at some point since b1804d3

Segfault reported here:
#14 (comment)

This repository snapshot works for me:
https://github.com/wanpinglee/MOSAIK/tree/b1804d3ae89915347c72cd7edfde4f585870b578

$ ./MosaikBuild -fr ../reads/bac/mycoplasma_genitali.fasta -oa mycoplasma_genitali.mskref
------------------------------------------------------------------------------
MosaikBuild 2.2.30                                                  2014-06-27
Wan-Ping Lee & Michael Stromberg  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting ../reads/bac/mycoplasma_genitali.fasta to a reference sequence archive.

- parsing reference sequences:
ref seqs: 1 (2.00 ref seqs/s)

- writing reference sequences:
100%[===================================================================================]      1.00 ref seqs/s        in  1 s  

- calculating MD5 checksums:
100%[===================================================================================]      1.00 ref seqs/s        in  1 s  

- writing reference sequence index:
100%[===================================================================================]      1.00 ref seqs/s        in  1 s  

- creating concatenated reference sequence:
100%[===================================================================================]      1.00 ref seqs/s        in  1 s  

- writing concatenated reference sequence...        finished.
- creating concatenated 2-bit reference sequence... finished.
- writing concatenated 2-bit reference sequence...  finished.

MosaikBuild CPU time: 0.021 s, wall time: 2.012 s

$ ./MosaikBuild -st 454 -q ../curesim/sim_mycoplasma_genitali_ind0_sub0.fastq -out sim_mycoplasma_genitali_ind0_sub0.mskreads
------------------------------------------------------------------------------
MosaikBuild 2.2.30                                                  2014-06-27
Wan-Ping Lee & Michael Stromberg  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- setting read group ID to: ZTK0O1H98OS
- setting sample name to: unknown
- setting sequencing technology to: 454

- parsing FASTQ file:
reads: 50,000 (49,950.0 reads/s)

Filtering statistics:
============================================
# reads written:             50000
# bases written:          19966537

MosaikBuild CPU time: 1.224 s, wall time: 1.309 s

$ ./MosaikAligner -ia mycoplasma_genitali.mskref -in sim_mycoplasma_genitali_ind0_sub0.mskreads -out mycoplasma_genitali_ind0_sub0.mosaik -annse 2.1.78.se.ann -annpe 2.1.78.pe.ann
------------------------------------------------------------------------------
MosaikAligner 2.2.30                                                2014-06-27
Wan-Ping Lee & Michael Stromberg  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 percent threshold of 0.15
- Using a Smith-Waterman bandwidth of 151
- Using an alignment candidate threshold of 55bp.
- Setting hash position threshold to 200
- Using a homo-polymer gap open penalty of 4
- loading reference sequence... finished.

Hashing reference sequence:
100%[==================================================================================] 386,193.1 ref bases/s        in  1 s  


Aligning read library (50000):
 0% [                                                                                      ]                                  \Segmentation fault (core dumped)