--no commit message

doc/sphinx/source/conf.py

@@ -203,7 +203,7 @@ latex_logo = 'OBITools.png'
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-latex_use_parts = False
+latex_use_parts = True
 
 # Additional stuff for the LaTeX preamble.
 #latex_preamble = ''

doc/sphinx/source/fastq.rst

@@ -143,36 +143,11 @@ file, but .fq and .fastq, are commonly used.
 See also
 --------
 
--  :ref:`fasta <fasta-classicalt>`__
+-  :ref:`fasta <classical-fasta>`
 
 References
 ----------
 
-.. raw:: mediawiki
-
-   {{reflist|2}}
-
-External links
---------------
-
--  `MAQ <http://maq.sourceforge.net/fastq.shtml>`__ webpage discussing
-   FASTQ variants
--  `Galaxy fastq
-   tools <http://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/>`__
--  `Fastx toolkit <http://hannonlab.cshl.edu/fastx_toolkit/>`__
-   collection of command line tools for Short-Reads FASTA/FASTQ files
-   preprocessing
--  `Fastqc <http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/>`__
-   quality control tool for high throughput sequence data
--  `PRINSEQ <http://prinseq.sourceforge.net/>`__ can be used for QC and
-   to filter, reformat, or trim sequence data (web-based and command
-   line versions)
-
-.. raw:: mediawiki
-
-   {{DEFAULTSORT:Fastq Format}}
-
-
 .. [1]
    Cock et al (2009) The Sanger FASTQ file format for sequences with
    quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids