Recent changes to patcheshttps://sourceforge.net/p/bowtie-bio/patches/2011-07-05T13:42:41ZRecent changes to patchesCrossbow: SOAPsnp parse error for parameter "-L"2011-07-05T13:42:41Z2011-07-05T13:42:41ZTully Ernsthttps://sourceforge.net/u/userid-1616560/https://sourceforge.netb13e2bd2b528ec83c7845eae505ae4ecf30d8516<div class="markdown_content"><p>The SOAPsnp contained within the crossbow release as an integer overflow due to the use of #atoi.<br />
This results in an inconsistent parameter -L (max read length) for values of 256 or greater (depends on compiler???)<br />
The uploaded files use long int and #atol to circumvent this problem. <br />
</p></div>Add RG:Z fields to alignment records with --sam-RG2011-03-08T14:40:29Z2011-03-08T14:40:29ZJohn Marshallhttps://sourceforge.net/u/jmarshall/https://sourceforge.net899bcc0ed65ef2ab3414235cdce0d85f01710a2d<div class="markdown_content"><p>The main reason for having an @RG header in a SAM file is so that (a subset of) the alignment records can be associated with it via their RG:Z: tagged fields. When --sam-RG options are used, bowtie should also add an RG: field to all alignment records printed, associating them with the specified @RG header. Thus the right thing happens when several bowtie output SAM files are merged, for example.</p>
<p>This BTW is what bwa samse/sampe -r does: it adds both an @RG header and RG:Z: fields to all output records. (But thanks for using a more convenient command line syntax that doesn't need large amounts of quoting!)</p>
<p>At first glance, it appears that it suffices to print out the extra field in sam.cpp's appendAligned() and reportUnOrMax(). If it is of use, I have attached a suggested patch for your consideration.</p>
<p>Thanks,</p>
<p>John Marshall<br />
<jm18@sanger.ac.uk></p></div>