Error with MosaikBuild reading FASTQ files with an empty line at the end of the file

[GoogleCodeExporter]

What steps will reproduce the problem?

1. Run the following command, using as an input a fastq file with an empty line 
at the end of the file:

./MosaikBuild -q test.fastq -out S test.dat -st 454

2. An error occurs!

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

MosaikBuild should build the internal format of the reads used as input.

Instead, the following error is output:

------------------------------------------------------------------------------
MosaikBuild 1.0.1388 
2010-02-01
Michael Stromberg                 Marth Lab, Boston College Biology 
Department
------------------------------------------------------------------------------

- setting read group ID to: ZCC6DSB2TT8
- setting sample name to: unknown
- setting sequencing technology to: 454
- trimming leading and lagging N's. Mates with >4 interior N's will be 
deleted.

- parsing FASTQ file:
reads: 0 |ERROR: Expected a '@' in the FASTQ header, found '
'.

What version of the product are you using? On what operating system?

Mosaik version 1.0.1388, running on Ubuntu Linux version 8.10 32bit.

Please provide any additional information below.

Use this sample fastq file to reproduce the error:

START
@SRR000853.1.1 EY1DSAR01ETQ99.1 length=134
TCAGATACTTATTAATGTTAACTTATTATGTTACTTTTATTTCCTCAATGGACAAAATTACAATTGATAATACAATGTTT
CTTTTGTTGCTGTAACTTTTGTAAGTACTGAAACAAGGGTAAAAGAAATAAACG
+SRR000853.1.1 EY1DSAR01ETQ99.1 length=134
<;;==<<:C=<D=B;98C=:0:D=9D==8:B;46GD8,<FB2:026;2<B;8<GC6(C=*=C<B;;:<C<:7<C=9<FB0
<GC8,;<3;<==:A9=FB5&:*>6;<8<;9FB28C=C?+<FB5'2FB2;FB1<<
@SRR000853.2.1 EY1DSAR01EQQS4.1 length=196
TCAGCATATCTTCGGCGATAGCTTTAGTCTCATTGTACGCATCCATAGGAACTTCTGGGATTGGCCAGGTTTCGTCTGCA
TTGTGCACATCTTGCCCATTAAAAATAACACCAGCAGAGGAAGTATATACAAGTATATTAACGCCACATTTCTTGCACAT
ATCTATCACGTTACGGGTTCCCTTAACATTCACTAT
+SRR000853.2.1 EY1DSAR01EQQS4.1 length=196
==<=<=<<=<B;=A9===<=<<D@-<<<<=<<B:<<=====<C<=<=B:C;<B;==C>*<C<B;C<<B:E@-<<<<=<;<
C<=<<==<<==C<=FB/=D=GC8.#<C===D=<===<<B;B;=<<<<<<<B;=<=<<B;C=<<B:;==D@-=C==<==:<
;<=<;=;<<=C<:<C?+B;C>*C<C<<<C<<;<<;=

END

If you remove last newline in the file, everything works smoothly.

Original issue reported on code.google.com by psil...@gmail.com on 24 Jun 2010 at 3:01

[GoogleCodeExporter]

Apologies, the line to reproduce the error should read:

./MosaikBuild -q test.fastq -out test.dat -st 454

An extra "S" slipped in there somehow!

Original comment by psil...@gmail.com on 24 Jun 2010 at 3:02

[GoogleCodeExporter]

The error-causing in FASTQ format as an attachment in this post, for 
convenience (and avoiding copy/paste errors as well).

Original comment by psil...@gmail.com on 24 Jun 2010 at 3:04

Attachments:

• test.fastq