Fixup # of index files in the manual/docs.

MANUAL

@@ -1359,7 +1359,7 @@ included with HISAT2, create a new temporary directory (it doesn't matter where)
     $HISAT2_HOME/hisat2-build $HISAT2_HOME/example/reference/22_20-21M.fa --snp $HISAT2_HOME/example/reference/22_20-21M.snp 22_20-21M_snp
 
 The command should print many lines of output then quit. When the command
-completes, the current directory will contain ten new files that all start with
+completes, the current directory will contain eight new files that all start with
 `22_20-21M_snp` and end with `.1.ht2`, `.2.ht2`, `.3.ht2`, `.4.ht2`, `.5.ht2`, `.6.ht2`,
 `.7.ht2`, and `.8.ht2`.  These files constitute the index - you're done!
 

MANUAL.markdown

@@ -2325,7 +2325,7 @@ included with HISAT2, create a new temporary directory (it doesn't matter where)
     $HISAT2_HOME/hisat2-build $HISAT2_HOME/example/reference/22_20-21M.fa --snp $HISAT2_HOME/example/reference/22_20-21M.snp 22_20-21M_snp
 
 The command should print many lines of output then quit. When the command
-completes, the current directory will contain ten new files that all start with
+completes, the current directory will contain eight new files that all start with
 `22_20-21M_snp` and end with `.1.ht2`, `.2.ht2`, `.3.ht2`, `.4.ht2`, `.5.ht2`, `.6.ht2`,
 `.7.ht2`, and `.8.ht2`.  These files constitute the index - you're done!
 

doc/manual.inc.html

@@ -1220,7 +1220,7 @@ <h1 id="getting-started-with-hisat2">Getting started with HISAT2</h1>
 <h2 id="indexing-a-reference-genome">Indexing a reference genome</h2>
 <p>To create an index for the genomic region (1 million bps from the human chromosome 22 between 20,000,000 and 20,999,999) included with HISAT2, create a new temporary directory (it doesn't matter where), change into that directory, and run:</p>
 <pre><code>$HISAT2_HOME/hisat2-build $HISAT2_HOME/example/reference/22_20-21M.fa --snp $HISAT2_HOME/example/reference/22_20-21M.snp 22_20-21M_snp</code></pre>
-<p>The command should print many lines of output then quit. When the command completes, the current directory will contain ten new files that all start with <code>22_20-21M_snp</code> and end with <code>.1.ht2</code>, <code>.2.ht2</code>, <code>.3.ht2</code>, <code>.4.ht2</code>, <code>.5.ht2</code>, <code>.6.ht2</code>, <code>.7.ht2</code>, and <code>.8.ht2</code>. These files constitute the index - you're done!</p>
+<p>The command should print many lines of output then quit. When the command completes, the current directory will contain eight new files that all start with <code>22_20-21M_snp</code> and end with <code>.1.ht2</code>, <code>.2.ht2</code>, <code>.3.ht2</code>, <code>.4.ht2</code>, <code>.5.ht2</code>, <code>.6.ht2</code>, <code>.7.ht2</code>, and <code>.8.ht2</code>. These files constitute the index - you're done!</p>
 <p>You can use <code>hisat2-build</code> to create an index for a set of FASTA files obtained from any source, including sites such as <a href="http://genome.ucsc.edu/cgi-bin/hgGateway">UCSC</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/genome">NCBI</a>, and <a href="http://www.ensembl.org/">Ensembl</a>. When indexing multiple FASTA files, specify all the files using commas to separate file names. For more details on how to create an index with <code>hisat2-build</code>, see the <a href="#the-hisat2-build-indexer">manual section on index building</a>. You may also want to bypass this process by obtaining a pre-built index.</p>
 <h2 id="aligning-example-reads">Aligning example reads</h2>
 <p>Stay in the directory created in the previous step, which now contains the <code>22_20-21M</code> index files. Next, run:</p>