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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._calldiff.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._join.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._junctiondiff.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._listtestvariants.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._listvariants.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._snpdiff.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._testing.pl
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._testvariants.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._varfilter.xml
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/._varfilter_wrapper.pl
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/calldiff.xml
--- a/cgatools/tools/cgatools/calldiff.xml Tue Jun 12 13:27:50 2012 -0400
+++ b/cgatools/tools/cgatools/calldiff.xml Tue Jun 12 13:28:37 2012 -0400
@@ -123,9 +123,9 @@
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/snpdiff.xml
--- a/cgatools/tools/cgatools/snpdiff.xml Tue Jun 12 13:27:50 2012 -0400
+++ b/cgatools/tools/cgatools/snpdiff.xml Tue Jun 12 13:28:37 2012 -0400
@@ -7,14 +7,75 @@
- cgatools snpdiff --beta -h
+ cgatools snpdiff
+ --reference $crr.fields.path
+ --variants $varfile
+ --genotypes $genotype
+ --output-prefix cg_
+ --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
-
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+ (report1 == 'Output')
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diff -r 9ab17046b3d8 -r 4f338a8e39b3 cgatools/tools/cgatools/testing.pl
--- a/cgatools/tools/cgatools/testing.pl Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/usr/bin/perl
-
-print "$0 @ARGV\n";
-open OUT, ">@ARGV[0]";
-print "test1 ok\ttest1 ok\ntest1 ok\ttest1 ok\n";
-print OUT "test ok\ttest ok\ntest ok\ttest ok\n";
-close OUT;
-open OUT, ">somefile";
-print OUT "test2 ok\ttest2 ok\ntest2 ok\ttest2 ok\n";
-close OUT;
\ No newline at end of file
diff -r 9ab17046b3d8 -r 4f338a8e39b3 listtestvariants.xml
--- a/listtestvariants.xml Tue Jun 12 13:27:50 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-
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- cgatools
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- cgatools listvariants
- --beta
- --reference ${crr.fields.path}
- --output $output1
- #if $include_list.listing == "yes"
- --variant-listing $include_list.list
- #end if
- $longvar
- --variants
- #if $file_types.data_sources.data_source == "in"
- #for $v in $file_types.data_sources.varfiles
- ${v.input}
- #end for
- #else
- `cat $file_types.data_sources.varlist`
- #end if
- ;
-
- cgatools testvariants
- --beta
- --reference ${crr.fields.path}
- --output $output2
- --input $output1
- --variants
- #if $file_types.data_sources.data_source == "in"
- #for $v in $file_types.data_sources.varfiles
- ${v.input}
- #end for
- #else
- `cat $file_types.data_sources.varlist`
- #end if
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-**What it does**
-
-This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
-
-cgatools: http://sourceforge.net/projects/cgatools/files/
-
------
-
-**cgatools Manual**::
-
- COMMAND NAME
- listvariants - Lists the variants present in a variant file.
-
- DESCRIPTION
- Lists all called variants present in the specified variant files, in a
- format suitable for processing by the testvariants command. The output is a
- tab-delimited file consisting of the following columns:
-
- variantId Sequential id assigned to each variant.
- chromosome The chromosome of the variant.
- begin 0-based reference offset of the beginning of the variant.
- end 0-based reference offset of the end of the variant.
- varType The varType as extracted from the variant file.
- reference The reference sequence.
- alleleSeq The variant allele sequence as extracted from the variant
- file.
- xRef The xRef as extrated from the variant file.
-
- OPTIONS
- -h [ --help ]
- Print this help message.
-
- --beta
- This is a beta command. To run this command, you must pass the --beta
- flag.
-
- --reference arg
- The reference crr file.
-
- --output arg (=STDOUT)
- The output file (may be omitted for stdout).
-
- --variants arg
- The input variant files (may be positional args).
-
- --variant-listing arg
- The output of another listvariants run, to be merged in to produce the
- output of this run.
-
- --list-long-variants
- In addition to listing short variants, list longer variants as well
- (10's of bases) by concatenating nearby calls.
-
- SUPPORTED FORMAT_VERSION
- 0.3 or later
-
-
-
- COMMAND NAME
- testvariants - Tests variant files for presence of variants.
-
- DESCRIPTION
- Tests variant files for presence of variants. The output is a tab-delimited
- file consisting of the columns of the input variants file, plus a column
- for each assembly results file that contains a character code for each
- allele. The character codes have meaning as follows:
-
- 0 This allele of this genome is consistent with the reference at this
- locus but inconsistent with the variant.
- 1 This allele of this genome has the input variant at this locus.
- N This allele of this genome has no-calls but is consistent with the
- input variant.
-
- OPTIONS
- -h [ --help ]
- Print this help message.
-
- --beta
- This is a beta command. To run this command, you must pass the --beta
- flag.
-
- --reference arg
- The reference crr file.
-
- --input arg (=STDIN)
- The input variants to test for.
-
- --output arg (=STDOUT)
- The output file (may be omitted for stdout).
-
- --variants arg
- The input variant files (may be passed in as arguments at the end of
- the command).
-
- SUPPORTED FORMAT_VERSION
- 0.3 or later
-
-