Apparently this never really rendered correctly

README.md

@@ -1,11 +1,11 @@
-#Bison: bisulfite alignment on nodes of a cluster.
+# Bison: bisulfite alignment on nodes of a cluster.
 
 **N.B.: There is now a tutorial available [here](http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download). This tutorial largely replaces this README file and users are encouraged to read it.**
 
 If you use Bison in your work please site the following:
 [Ryan D.P. and Ehninger D. **Bison: bisulfite alignment on nodes of a cluster.** *BMC Bioinformatics* 2014, Oct 18;**15**(1):337](http://www.biomedcentral.com/1471-2105/15/337)
 
-##Usage
+## Usage
 
 One can index all fasta files (files with extension .fa or .fasta) in a
 directory as follows:
@@ -66,11 +66,12 @@ judgement).
 
 See the "Auxiliary files" section, below, for additional files.
 
-##Auxiliary files
+## Auxiliary files
 
 The following programs and scripts will be available if you type "make auxiliary":
 
-###bedGraph2BSseq.py
+### bedGraph2BSseq.py
+
 This python script can accept a filename prefix and the names of at least 2
 bedGraph files and output 3 files for input into BSseq. A single chromosome can
 be processed at a time, if desired, by using the -chr option. The output files
@@ -94,18 +95,18 @@ BS1 <- BSseq(M=M, Cov=Cov, gr=gr, pData=groups, sampleNames=colnames(M)) #You'll
 ```
 
 
-###`bedGraph2methylKit`
+### `bedGraph2methylKit`
 As above, but each bedGraph file is converted to a .methylKit file. The
 bedGraphs should be of CpGs and not have had the strands merged (i.e., don't run
 the merge_CpGs command below).
 
-###`bedGraph2MOABS`
+### `bedGraph2MOABS`
 Like `bedGraph2methylKit`, but each bedGraph file is converted to a .moabs file.
 The bedGraph files should ideally contain single-C metrics rather than having
 been merged to form CpG metrics, though both are supported. The resulting .moabs
 files can then be used by `mcomp` in the MOABS package.
 
-###`bedGraph2MethylSeekR`
+### `bedGraph2MethylSeekR`
 As above, but each bedGraph file is converted into a .MethylSeekR file. The
 bedGraphs MUST be merged before-hand with bison_merge_CpGs to create per-CpG
 metrics, as this is what MethylSeekR is expecting. Input is performed with the
@@ -121,17 +122,17 @@ names(chromosome_lengths) <- fai$V1
 d <- readMethylome("file.MethylSeekR", chromosome_lengths)
 ```
 
-###`make_reduced_genome`
+### `make_reduced_genome`
 Create a reduced representation genome appropriate for reads of a given size
 ($size, default is 36bp). MspI and TaqI libraries are supported. Nucleotides
 greater than $size+10% are converted to N.
 
-###`merge_bedGraphs.py`
+### `merge_bedGraphs.py`
 This will merge bedGraphs from technical replicates of a single sample into a
 single bedGraph file, summing the methylation metrics as it goes. The output,
 like the input is coordinate sorted.
 
-###`bison_merge_CpGs`
+### `bison_merge_CpGs`
 Methylation is usually symmetric at CpG sites. While the output bedGraph files
 have a single-C resolution, this will convert that to single-CpG resolution by
 summing Cs in the same CpG from opposite strands. This saves space and will
@@ -143,7 +144,7 @@ packages either do not require a helper script or can use one of the
 aforementioned scripts. Import instructions for such packages are mentioned
 below.
 
-###BiSeq
+### BiSeq
 BiSeq requires input in an identical format as BSseq. Consequently, just use the
 bedGraph2BSseq.py helper script. The following example commands should then
 suffice to load everything into R:
@@ -159,7 +160,7 @@ groups <- DataFrame(row.names=colnames(M),
 d <- BSraw(exptData=exptData, rowData=gr, colData=groups, totalReads=Cov, methReads=M)
 ```
 
-###BEAT
+### BEAT
 The BEAT Bioconductor package conveniently expects per-sample position and
 methylation information in a format already present in bedGraph files. However,
 this information is in a slightly different format than bedGraph, so the
@@ -169,7 +170,7 @@ sample_name.positions.csv.
     awk '{if(NR>1){printf("%s,%i,%i,%i\n",$1,$2+1,$5,$6)}else{printf("chr,pos,meth,unmeth\n")}}' sample.bedGraph > sample.positions.csv
 
 
-##Advanced bison_herd usage
+## Advanced bison_herd usage
 
 `bison_herd` has the ability to use a semi-arbitrary number of nodes. In practice,
 if bison is given N nodes, it will effectively use `2*((N-1)/2)+1` or
@@ -222,7 +223,7 @@ Even when --reorder is used, if there is >1 second between these, then you may
 benefit from increasing the number of compression threads. For those curious,
 this option is identical to that used in samtools.
 
-##Throttling
+## Throttling
 
 `bison_herd` generally uses blocking, but not synchronous sends. What this means
 in practice is that many reads will be queued by the master node for sending to
@@ -245,7 +246,7 @@ Throttling is not always required, particularly as an increasing number of nodes
 are used. Throttling can be disabled altogether by compiling with -DNOTHROTTLE,
 which will remove all related components.
 
-##Debug mode
+## Debug mode
 
 For debugging, a special debug mode is available for both bison and `bison_herd`
 by compiling with -DDEBUG. Instead of running of needing multiple nodes, both
@@ -266,24 +267,24 @@ non-directional reads.
 In general, this mode should not be used unless you are running into extremely
 odd bugs.
 
-##Compatibility with Bismark
+## Compatibility with Bismark
 
 Bison is generally similar to bismark, however the indexes are incompatible,
 due to bismark renaming contigs. Also, the two will not produce identical 
 output, due to algorithmic differences. Running `bison_methylation_extractor`
 on the output of bismark will also produce different results, again due to
 algorithmic differences. In addition, bison always outputs BAM files directly.
 
-##Other details
+## Other details
 
 Bison needn't be run on multiple computers. You can also use a single
 computer for all compute nodes (e.g. mpiexec -n 5 bison ...). The same holds
 true for `bison_herd`. Both bison and `bison_herd` seem to be faster than bismark,
 even when limited to the same resources.
 
-##Changes
+## Changes
 
-###0.4.0
+### 0.4.0
 
   *  Allow lower case reads in fastq files (previously, this would result in
      corrupt BAM files.
@@ -311,15 +312,15 @@ even when limited to the same resources.
   *  Fixed a bug in bison_CpG_coverage, where previously only the first
      chromosome was used.
 
-###0.3.3
+### 0.3.3
 
   *  Allow mixed and discordant alignments.
 
-###0.3.2b
+### 0.3.2b
 
   *  Fix the Makefile to use the static htslib library.
 
-###0.3.2
+### 0.3.2
   *  Added bedGraph2MOABS to convert bedGraph files for use by MOABS. See usage
      above.
 
@@ -335,7 +336,7 @@ even when limited to the same resources.
   *  The default minimum MAPQ and Phred scores used by `bison_mbias` have been
      updated to match `bison_methylation_extractor`.
 
-###0.3.1
+### 0.3.1
   *  The various bedGraph files didn't previously have a "track" line. The UCSC
      Genome Browser requires this, so bedGraph files produced will now contain 
      it. It should be noted that this is the very minimal line required. Bison
@@ -355,7 +356,7 @@ even when limited to the same resources.
      MAPQ, this one will do that for the read/pair with the highest summed phred
      score (a la picard).
 
-###0.3.0
+### 0.3.0
   *  Note: The indices produced by previous versions are not guaranteed to be
      compatible unless you used a multi-fasta file. There was a serious
      implementation problem with how `bison_index` worked when given multiple
@@ -387,7 +388,7 @@ even when limited to the same resources.
 
   *  A number of small bug fixes, such as when "genome_dir" doesn't end in a /.
 
-###0.2.4
+### 0.2.4
   *  Fixed an off-by-one error in bison_mbias. Also, at some point 1-methylation
      percentage started getting calculated. That's been fixed.
 
@@ -399,7 +400,7 @@ even when limited to the same resources.
      single-C bedGraph files before (if they were merged, then they were being
      handled correctly).
 
-###0.2.3
+### 0.2.3
   *  Fix how hard and soft-clipped bases are dealt with (previously, soft-
      clipped bases resulted in an error and hard-clipped bases in incorrect
      position assignments!).
@@ -429,15 +430,15 @@ even when limited to the same resources.
      (effectively the more verbose version of the MD tag) contains soft-clipped
      sequences. I could probably have these removed if someone would like.
 
-###0.2.2
+### 0.2.2
   *  Properly fixed some wording on the textual output (i.e., removed the word
      "unique").
 
   *  Lowered the default MAPQ and Phred thresholds used by the methylation
      extractor to 10 each. That the MAPQ threshold was originally
      20 was an error on my part.
 
-###0.2.1
+### 0.2.1
   *  Added support for file globbing in bison_herd. You may now input multiple
      files using a combination of wild-cards (*, ?, etc.) and commas. Remember
      to put these in quotes (e.g., "foo/*1.fq.gz","bar/*1.fq.gz") so the shell
@@ -484,7 +485,7 @@ even when limited to the same resources.
 
   *  Fixed a bug in bison_herd that allowed early termination without warning.
 
-###0.2.0
+### 0.2.0
   *  Added a note to the methylation summary statistics output at the end of a
      run that the numbers will include double counting of any site covered by
      both mates in a pair. These metrics are only meant for general information
@@ -512,7 +513,7 @@ even when limited to the same resources.
      actually supports the level of thread support requested (previously, this
      was just assumed).
 
-###0.1.1
+### 0.1.1
   *  Fixed a number of minor bugs.
 
   *  Added support for uncompressed fastq files, as well as bzipped files
@@ -545,5 +546,5 @@ even when limited to the same resources.
      an RRBS genome and other possibly useful functions.
 
 
-###0.1.0
+### 0.1.0
   Initial release