Mercurial > repos > bonsai > crac
changeset 4:ac6be31420fe draft
Uploaded
| author | bonsai |
|---|---|
| date | Fri, 13 Sep 2013 10:36:13 -0400 |
| parents | 4cf2808854bc |
| children | 46d61dc5c92e |
| files | crac.xml |
| diffstat | 1 files changed, 57 insertions(+), 57 deletions(-) [+] |
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--- a/crac.xml Fri Sep 13 10:01:00 2013 -0400 +++ b/crac.xml Fri Sep 13 10:36:13 2013 -0400 @@ -157,109 +157,109 @@ ------ crac 1.3.0 Compiled on Sep 13 2013. - -h, --help <none> print this help and exit - -f, --full-help <none> print a complete help and exit - -v <none> print version and exit + -h, --help <none> print this help and exit + -f, --full-help <none> print a complete help and exit + -v <none> print version and exit Mandatory arguments - -i <FILE> set genome index file (without the extension filename) - -r <FILE> [FILE2] set read file. Specify FILE2 in case of paired-end reads - -k <INT> set k-mer length - -o, --sam <FILE> set SAM output filename or print on STDOUT with "-o -" argument + -i <FILE> set genome index file (without the extension filename) + -r <FILE> [FILE2] set read file. Specify FILE2 in case of paired-end reads + -k <INT> set k-mer length + -o, --sam <FILE> set SAM output filename or print on STDOUT with "-o -" argument Optional arguments * Protocol - --stranded <none> set the read mapping with for a strand specific library (DEFAULT non-strand specific) + --stranded <none> set the read mapping with for a strand specific library (DEFAULT non-strand specific) * Efficiency - --nb-threads <INT> set the number of worker threads (DEFAULT 1) - --read-length, -m <INT> set read length in case of all reads have the same length to optimize + --nb-threads <INT> set the number of worker threads (DEFAULT 1) + --read-length, -m <INT> set read length in case of all reads have the same length to optimize CPU and memory times - --treat-multiple <none> consider alignments with multiple locations (>max-duplication) rather than considering a no-alignment in the SAM file - --max-locs <INT> set the maximum number of locations on the reference index (DEFAULT 300) + --treat-multiple <none> consider alignments with multiple locations (>max-duplication) rather than considering a no-alignment in the SAM file + --max-locs <INT> set the maximum number of locations on the reference index (DEFAULT 300) * Accuracy - --no-ambiguity <none> discard biological events (splice, snv, indel, chimera) which have several matches on the reference index + --no-ambiguity <none> discard biological events (splice, snv, indel, chimera) which have several matches on the reference index Optional output arguments - --all <FILE> set output base filename for all causes following - --gz <none> all output files specified after this argument are gzipped + --all <FILE> set output base filename for all causes following + --gz <none> all output files specified after this argument are gzipped * Summary and statistics - --summary <FILE> set output summary file + --summary <FILE> set output summary file * Mapping - --single <FILE> set output single file - --duplicate <FILE> set output duplication file - --multiple <FILE> set output multiple file - --none <FILE> set output none file - --normal <FILE> set output normal file - --almost-normal <FILE> set output almost normal file + --single <FILE> set output single file + --duplicate <FILE> set output duplication file + --multiple <FILE> set output multiple file + --none <FILE> set output none file + --normal <FILE> set output normal file + --almost-normal <FILE> set output almost normal file * Biological causes - --snv <FILE> set output SNV file - --indel <FILE> set output short indel file - --splice <FILE> set output splice junction file - --weak-splice <FILE> set output coverless splice junction file - --chimera <FILE> set output chimera junction file - --paired-end-chimera <FILE> set output for paired-end chimera file - --biological <FILE> set output bio-undetermined file + --snv <FILE> set output SNV file + --indel <FILE> set output short indel file + --splice <FILE> set output splice junction file + --weak-splice <FILE> set output coverless splice junction file + --chimera <FILE> set output chimera junction file + --paired-end-chimera <FILE> set output for paired-end chimera file + --biological <FILE> set output bio-undetermined file * Sequence errors - --errors <FILE> set output sequence errors file + --errors <FILE> set output sequence errors file * Repetition - --repeat <FILE> set output repetition file + --repeat <FILE> set output repetition file * Other causes - --undetermined <FILE> set output undetermined file - --nothing <FILE> set output nothing file + --undetermined <FILE> set output undetermined file + --nothing <FILE> set output nothing file Optional process for specific research - --deep-snv <none> will search hard to find SNPs - --stringent-chimera <none> will search chimeras with more accuracy (but less sensitivity) + --deep-snv <none> will search hard to find SNPs + --stringent-chimera <none> will search chimeras with more accuracy (but less sensitivity) Optional process launcher (once must be selected) * Exact matching tool - --emt <none> launch CRAC-emt for exact mapping of short reads + --emt <none> launch CRAC-emt for exact mapping of short reads * Server tool (for debugging) - --server <none> launch CRAC server,the output arguments will + --server <none> launch CRAC server,the output arguments will not be taken into account - --input-name-server <STRING> DEFAULT classify.fifo - --output-name-server <STRING> DEFAULT classify.out.fifo + --input-name-server <STRING> DEFAULT classify.fifo + --output-name-server <STRING> DEFAULT classify.out.fifo Additional settings for users * Sam output file - --detailed-sam <none> more informations are added in SAM output file + --detailed-sam <none> more informations are added in SAM output file * Mapping - --min-percent-single-loc <FLOAT> DEFAULT 0.15 - --min-duplication <INT> DEFAULT 2 - --max-duplication <INT> DEFAULT 9 - --min-percent-duplication-loc <FLOAT> DEFAULT 0.15 - --min-percent-multiple-loc <FLOAT> DEFAULT 0.50 - --min-repetition <INT> DEFAULT 20 - --min-percent-repetition-loc <FLOAT> DEFAULT 0.20 + --min-percent-single-loc <FLOAT> DEFAULT 0.15 + --min-duplication <INT> DEFAULT 2 + --max-duplication <INT> DEFAULT 9 + --min-percent-duplication-loc <FLOAT> DEFAULT 0.15 + --min-percent-multiple-loc <FLOAT> DEFAULT 0.50 + --min-repetition <INT> DEFAULT 20 + --min-percent-repetition-loc <FLOAT> DEFAULT 0.20 * Biological causes - --max-splice-length <INT> DEFAULT 300000 - --max-paired-end-length <INT> DEFAULT 300000 - --max-bio-indel <INT> DEFAULT 15 - --max-bases-retrieved <INT> DEFAULT 15 + --max-splice-length <INT> DEFAULT 300000 + --max-paired-end-length <INT> DEFAULT 300000 + --max-bio-indel <INT> DEFAULT 15 + --max-bases-retrieved <INT> DEFAULT 15 * Undetermined - --min-support-no-cover <FLOAT> DEFAULT 1.30 + --min-support-no-cover <FLOAT> DEFAULT 1.30 Additional settings for advanced users * Break verification and fusion (merging mirage breaks) - --min-break-length <FLOAT> DEFAULT 0.50 - --max-bases-randomly-matched <INT> DEFAULT 10 - --max-extension-length <INT> DEFAULT 10 + --min-break-length <FLOAT> DEFAULT 0.50 + --max-bases-randomly-matched <INT> DEFAULT 10 + --max-extension-length <INT> DEFAULT 10 * Threading - --nb-tags-info-stored <INT> DEFAULT 1000 + --nb-tags-info-stored <INT> DEFAULT 1000 * Deep SNV search option - --nb-nucleotides-snv-comparison <INT> DEFAULT 8 + --nb-nucleotides-snv-comparison <INT> DEFAULT 8 </help> </tool>