Patches

This is a list of patches I've created for various software. Unfortunately not all have been included into mainstream distributions, for many reasons... But don't worry! They should not harm your system (but you never know... ^__^). I will remove any patch as soon as it is integrated to mainstream code.
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clover-2010-02-19-omp.patch
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Patch to add OpenMP support to clover. This enables multicore processing with modern compilers. This patch applies to clover-2010-02-19.  11k v. 1 Jan 3, 2011, 2:40 PM Davide Cittaro
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maq-ill2sanger.patch
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This patch adds to maq 0.7.1 capabilities to convert from Illumina GA 1.3+ fastq to Sanger fastq.  3k v. 1 Sep 17, 2009, 12:21 PM Davide Cittaro
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mb_64bit-safe.patch
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This patch allows mrbayes 3.1.2 run on 64 bit platforms. You can find MrBayes here http://mrbayes.csit.fsu.edu/ but the software is apparently no more developed...  82k v. 3 Sep 17, 2009, 12:26 PM Davide Cittaro
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mfinder.patch
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This patch should allow you to run mfinder (http://www.weizmann.ac.il/mcb/UriAlon/groupNetworkMotifSW.html) safely on any UNIX system  5k v. 1 Sep 17, 2009, 12:20 PM Davide Cittaro
 Accepted Patches
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MACS-1.3.6.1_sam_bam_p2.patch
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This patch adds SAM and BAM support to MACS (http://liulab.dfci.harvard.edu/MACS/)  13k v. 2 Oct 5, 2009, 11:35 AM Davide Cittaro
 Old patches
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bwa-0.5.8a-illumina-qualities.patch
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Adds an option at bwa aln to use Illumina quality scale as input files. Qualities are converted to Sanger format on the fly.  5k v. 2 Dec 22, 2010, 6:48 AM Davide Cittaro
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bwa-svn-r50_illumina-qual.patch
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Updated patch for Illumina qualities support in bwa aln. This patch has been developed for bwa svn version (revision 50).  4k v. 2 Jan 25, 2011, 5:57 AM Davide Cittaro
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clover-omp.patch
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This patch adds OpenMP support for clover (http://zlab.bu.edu/clover/). Source should be compiled with an OpenMP capable C++ compiler.   11k v. 5 Jan 3, 2011, 2:36 PM Davide Cittaro
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samtools-0.1.7-17_illumina-qualities.patch
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SAM/BAM files with Solexa or Illumina qualities can be converted to Sanger qualities in "view" predicate  2k v. 2 Dec 22, 2010, 6:49 AM Davide Cittaro
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samtools-mpfr.patch
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Patch to add support to MPFR to samtools cns functions and replaces logl() and expl() functions.  10k v. 2 Dec 22, 2010, 6:49 AM Davide Cittaro
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