#27 Error

[Daniel Cameron]

Inconsistent handling of fasta header comments results in a fatal error when running mrfast against a reference containing fasta header.

Error Message:
35439200 sequences are read in 248.93. (0 discarded) [Mem:15869.31 M]

---

| Genome Name | Loading Time | Mapping Time | Memory Usage(M) | Total Mappings Mapped reads |

Error: Cannot Open the file ~/workspace/1 dna:chromosome chromosome:GRCh37:1:1:249250621:130f73bdf2efe564a958f359fb75e3623.output01.tmp

Relevant info:
The first line of the reference in question is:

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
The file ~/workspace/130f73bdf2efe564a958f359fb75e3623.output01.tmp exists (so at least part of the program is treating fasta headers correctly)

Steps to reproduce:
1) Download and decompress ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
2) Generate sample fastq using read simulator
3) Run mrfast against simulated reads

[Daniel Cameron]

Without markdown transformation:

    `>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1`

    `Error: Cannot Open the file ~/workspace/__1 dna:chromosome chromosome:GRCh37:1:1:249250621:1__30f73bdf2efe564a958f359fb75e3623.output__0__1.tmp`

    `~/workspace/__1__30f73bdf2efe564a958f359fb75e3623.output__0__1.tmp` does exist