[galaxy-dev] [hg] galaxy 3565: Added new tabular/pileup join tool and associa...

16 Apr 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/3ac95cd927d7
changeset: 3565:3ac95cd927d7
user:      Kelly Vincent <kpvincent@bx.psu.edu>
date:      Fri Mar 26 12:00:55 2010 -0400
description:
Added new tabular/pileup join tool and associated test files. Also added pileup datatype.

diffstat:

 datatypes_conf.xml.sample              |     2 +
 lib/galaxy/datatypes/registry.py       |     3 +
 lib/galaxy/datatypes/tabular.py        |    93 ++
 lib/galaxy/datatypes/test/10col.pileup |    30 +
 lib/galaxy/datatypes/test/6col.pileup  |    30 +
 test-data/1.pileup                     |  1000 ++++++++++++++++++++++++++++++++
 test-data/column_join_in1.pileup       |    30 +
 test-data/column_join_in2.pileup       |    30 +
 test-data/column_join_in3.pileup       |    30 +
 test-data/column_join_in4.pileup       |    25 +
 test-data/column_join_in5.pileup       |    25 +
 test-data/column_join_in6.pileup       |    25 +
 test-data/column_join_in7.pileup       |    32 +
 test-data/column_join_in8.pileup       |    23 +
 test-data/column_join_in9.pileup       |    25 +
 test-data/column_join_out1.pileup      |    60 +
 test-data/column_join_out2.pileup      |    65 ++
 test-data/column_join_out3.pileup      |    70 ++
 test/functional/test_get_data.py       |    17 +
 tool_conf.xml.sample                   |     1 +
 20 files changed, 1616 insertions(+), 0 deletions(-)

diffs (1743 lines):

diff -r 5f927f52191c -r 3ac95cd927d7 datatypes_conf.xml.sample

--- a/datatypes_conf.xml.sample	Fri Mar 26 09:51:03 2010 -0400
+++ b/datatypes_conf.xml.sample	Fri Mar 26 12:00:55 2010 -0400
@@ -61,6 +61,7 @@
             <converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
         </datatype>
         <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+        <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
         <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
         <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
         <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
@@ -239,6 +240,7 @@
         <sniffer type="galaxy.datatypes.interval:CustomTrack"/>
         <sniffer type="galaxy.datatypes.interval:Gff"/>
         <sniffer type="galaxy.datatypes.interval:Gff3"/>
+        <sniffer type="galaxy.datatypes.tabular:Pileup"/>
         <sniffer type="galaxy.datatypes.interval:Interval"/>
         <sniffer type="galaxy.datatypes.tabular:Sam"/>
     </sniffers>
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py	Fri Mar 26 09:51:03 2010 -0400
+++ b/lib/galaxy/datatypes/registry.py	Fri Mar 26 12:00:55 2010 -0400
@@ -155,6 +155,7 @@
                 'laj'         : images.Laj(),
                 'lav'         : sequence.Lav(),
                 'maf'         : sequence.Maf(),
+                'pileup'      : tabular.Pileup(),
                 'qualsolid'   : qualityscore.QualityScoreSOLiD(),
                 'qualsolexa'  : qualityscore.QualityScoreSolexa(),
                 'qual454'     : qualityscore.QualityScore454(),
@@ -185,6 +186,7 @@
                 'laj'         : 'text/plain',
                 'lav'         : 'text/plain',
                 'maf'         : 'text/plain',
+                'pileup'      : 'text/plain',
                 'qualsolid'   : 'text/plain',
                 'qualsolexa'  : 'text/plain',
                 'qual454'     : 'text/plain',
@@ -218,6 +220,7 @@
                 interval.CustomTrack(),
                 interval.Gff(),
                 interval.Gff3(),
+                tabular.Pileup(),
                 interval.Interval(),
                 tabular.Sam()
             ]
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py	Fri Mar 26 09:51:03 2010 -0400
+++ b/lib/galaxy/datatypes/tabular.py	Fri Mar 26 12:00:55 2010 -0400
@@ -327,3 +327,96 @@
         except:
             pass
         return False
+
+class Pileup( Tabular ):
+    """Tab delimited data in pileup (6- or 10-column) format"""
+    file_ext = "pileup"
+
+    """Add metadata elements"""
+    MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
+    MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )
+    MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter )
+
+    def init_meta( self, dataset, copy_from=None ):
+        Tabular.init_meta( self, dataset, copy_from=copy_from )
+
+    def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            if line_count is None:
+                # See if line_count is stored in the metadata
+                if dataset.metadata.data_lines:
+                    dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) )
+                else:
+                    # Number of lines is not known ( this should not happen ), and auto-detect is
+                    # needed to set metadata
+                    dataset.blurb = "? genomic coordinates"
+            else:
+                dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def make_html_table( self, dataset, skipchars=[] ):
+        """Create HTML table, used for displaying peek"""
+        out = ['<table cellspacing="0" cellpadding="3">']
+        comments = []
+        try:
+            # Generate column header
+            out.append('<tr>')
+            for i in range( 1, dataset.metadata.columns+1 ):
+                if i == dataset.metadata.chromCol:
+                    out.append( '<th>%s.Chrom</th>' % i )
+                elif i == dataset.metadata.startCol:
+                    out.append( '<th>%s.Start</th>' % i )
+                elif i == dataset.metadata.baseCol:
+                    out.append( '<th>%s.Base</th>' % i )
+                else:
+                    out.append( '<th>%s</th>' % i )
+            out.append('</tr>')
+            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
+            out.append( '</table>' )
+            out = "".join( out )
+        except Exception, exc:
+            out = "Can't create peek %s" % str( exc )
+        return out
+
+    def repair_methods( self, dataset ):
+        """Return options for removing errors along with a description"""
+        return [ ("lines", "Remove erroneous lines") ]
+
+    def sniff( self, filename ):
+        """
+        Checks for 'pileup-ness'
+
+        There are two main types of pileup: 6-column and 10-column. For both, 
+        the first three and last two columns are the same. We only check the
+        first three to allow for some personalization of the format.
+
+        >>> fname = get_test_fname( 'interval.interval' )
+        >>> Pileup().sniff( fname )
+        False
+        >>> fname = get_test_fname( '6col.pileup' )
+        >>> Pileup().sniff( fname )
+        True
+        >>> fname = get_test_fname( '10col.pileup' )
+        >>> Pileup().sniff( fname )
+        True
+        """
+        headers = get_headers( filename, '\t' )
+        try:
+            for hdr in headers:
+                if hdr and not hdr[0].startswith( '#' ):
+                    if len( hdr ) < 3:
+                        return False
+                    try:
+                        # chrom start in column 1 (with 0-based columns)
+                        # and reference base is in column 2
+                        check = int( hdr[1] )
+                        assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ]
+                    except:
+                        return False
+            return True
+        except:
+            return False
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/10col.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/10col.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM	1	G	G	25	0	25	1	^:.	I
+chrM	2	T	T	25	0	25	1	.	I
+chrM	3	T	T	25	0	25	1	.	I
+chrM	4	A	A	36	0	25	3	.^:.^:.	II+
+chrM	5	A	A	36	0	25	3	...	III
+chrM	6	T	T	36	0	25	3	...	III
+chrM	7	G	G	42	0	25	5	...^:.^:.	IIIII
+chrM	8	T	T	45	0	25	6	.....^:.	IIIIII
+chrM	9	A	A	51	0	25	8	......^:.^:.	IIIIIIII
+chrM	10	G	G	54	0	25	9	........^:.	IIIIIIIII
+chrM	11	C	C	57	0	25	10	.........^:.	IIIIIIIIII
+chrM	12	T	T	60	0	25	11	..........^:.	IIIIIIIIIII
+chrM	13	T	T	78	0	25	17	...........^:.^:.^:.^:.^:.^:.	IIIIIIIIIIIIIIIII
+chrM	14	A	A	56	0	25	18	.......G.........^:.	BIIIIIII+IIIIIIIII
+chrM	15	A	A	87	0	25	20	..................^:.^:.	DIIIIIII(IIIIIIIIIII
+chrM	16	T	T	87	0	25	20	....................	IIIIIIIIIIIIIIIIIIII
+chrM	17	A	A	87	0	25	20	....................	9IIIIIIIIIIIIIIIIIII
+chrM	18	A	A	87	0	25	20	....................	@IIIIIIIIIIIIIIIIIII
+chrM	19	T	T	55	0	25	20	..................GG	IIIIIIIIIIIIIIIIII'A
+chrM	20	A	A	54	0	25	20	..................C.	IIIIIIIIIIIIIII2II#$
+chrM	21	T	T	87	0	25	20	....................	IIIIIIIIIIIIIIIIIIII
+chrM	22	A	A	87	0	25	20	....................	IIIIIIIIIIIIIIAIIIII
+chrM	23	A	A	87	0	25	20	....................	9IIIIIIIIII0IIIIIIII
+chrM	24	A	A	87	0	25	20	........N...........	IIIIIIII"IIIIICIIIII
+chrM	25	G	G	57	0	25	21	...A................^:.	A@.$IIIIIIIFIIIIIIIII
+chrM	26	C	C	57	0	25	21	.......A.............	IIHIDII&IIIIIIIIIIIII
+chrM	27	A	A	99	0	25	24	.....................^:.^:.^:.	IE8IFIII9IIIIIIIIIIIIIII
+chrM	28	A	A	99	0	25	24	........................	1FIIIIIIIIIIIIIIIIDEIIII
+chrM	29	G	G	55	0	25	24	..................NN....	;IIIIII+HII=IIIIII""IIII
+chrM	30	G	G	68	0	25	25	...C....................^:.	;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/6col.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/6col.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM	42	C	1	^:.	I
+chrM	43	C	2	.^:.	II
+chrM	44	T	2	..	II
+chrM	45	A	3	..^:.	III
+chrM	46	G	4	...^:.	IIII
+chrM	47	A	5	....^:,	IIIII
+chrM	48	T	5	....,	IIIII
+chrM	49	G	5	....,	IIIII
+chrM	50	A	5	....,	IIIII
+chrM	51	G	5	....,	IIIII
+chrM	52	T	5	....,	IIIII
+chrM	53	A	5	....,	IIIII
+chrM	54	T	5	....,	IIIII
+chrM	55	T	5	....,	IIIII
+chrM	56	C	5	....,	IIIII
+chrM	57	T	5	....,	IIIII
+chrM	58	T	5	....,	IIIII
+chrM	59	A	5	....,	IIIII
+chrM	60	C	5	....,	IIIII
+chrM	61	T	5	....,	IIIII
+chrM	62	C	5	....,	IIIII
+chrM	63	C	5	....,	IIIII
+chrM	64	A	5	....,	IIIII
+chrM	65	T	5	....,	IIIII
+chrM	66	A	5	....,	IIIII
+chrM	67	A	5	....,	IIIII
+chrM	68	A	5	....,	IIICI
+chrM	69	C	5	....,	IIIII
+chrM	70	A	5	....,	IIIII
+chrM	71	C	5	....,	IIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/1.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,1000 @@
+chrM	42	C	1	^:.	I
+chrM	43	C	2	.^:.	II
+chrM	44	T	2	..	II
+chrM	45	A	3	..^:.	III
+chrM	46	G	4	...^:.	IIII
+chrM	47	A	5	....^:,	IIIII
+chrM	48	T	5	....,	IIIII
+chrM	49	G	5	....,	IIIII
+chrM	50	A	5	....,	IIIII
+chrM	51	G	5	....,	IIIII
+chrM	52	T	5	....,	IIIII
+chrM	53	A	5	....,	IIIII
+chrM	54	T	5	....,	IIIII
+chrM	55	T	5	....,	IIIII
+chrM	56	C	5	....,	IIIII
+chrM	57	T	5	....,	IIIII
+chrM	58	T	5	....,	IIIII
+chrM	59	A	5	....,	IIIII
+chrM	60	C	5	....,	IIIII
+chrM	61	T	5	....,	IIIII
+chrM	62	C	5	....,	IIIII
+chrM	63	C	5	....,	IIIII
+chrM	64	A	5	....,	IIIII
+chrM	65	T	5	....,	IIIII
+chrM	66	A	5	....,	IIIII
+chrM	67	A	5	....,	IIIII
+chrM	68	A	5	....,	IIICI
+chrM	69	C	5	....,	IIIII
+chrM	70	A	5	....,	IIIII
+chrM	71	C	5	....,	IIIII
+chrM	72	A	5	....,	IAIII
+chrM	73	T	5	....,	IIIII
+chrM	74	A	5	....,	IIIII
+chrM	75	G	5	....,	%IIII
+chrM	76	G	5	T...,	*IIII
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+chrM	89	C	2	..	II
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+chrM	118	A	2	.$.$	F8
+chrM	156	T	1	^:,	&
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+chrM	268	A	4	,...	EIII
+chrM	269	A	4	,...	=III
+chrM	270	C	4	a...	;III
+chrM	271	G	4	,...	;III
+chrM	272	A	4	,...	8@II
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+chrM	295	A	3	.,.	4II
+chrM	296	T	3	.,.	III
+chrM	297	A	3	.,.	BII
+chrM	298	A	3	.,.	CII
+chrM	299	G	3	.,.	III
+chrM	300	G	3	.,.	;II
+chrM	301	G	3	.,.	III
+chrM	302	T	3	.$,.	III
+chrM	303	T	2	,.	II
+chrM	304	G	2	,.	II
+chrM	305	G	2	,.	II
+chrM	306	T	2	,.	II
+chrM	307	A	2	,.	II
+chrM	308	A	2	,.	II
+chrM	309	A	2	,.	II
+chrM	310	T	2	,.	II
+chrM	311	T	2	,.	II
+chrM	312	T	3	,.^:.	III
+chrM	313	C	3	,..	III
+chrM	314	G	3	,..	III
+chrM	315	T	3	,..	III
+chrM	316	G	3	,..	III
+chrM	317	C	3	,..	III
+chrM	318	C	3	,..	III
+chrM	319	A	3	,$..	III
+chrM	320	G	2	..	II
+chrM	321	C	2	.$.	II
+chrM	322	C	1	.	I
+chrM	323	A	1	.	I
+chrM	324	C	1	.	I
+chrM	325	C	1	.	I
+chrM	326	G	1	.	I
+chrM	327	C	1	.	I
+chrM	328	G	1	.	I
+chrM	329	G	1	.	I
+chrM	330	T	1	.	I
+chrM	331	C	1	.	I
+chrM	332	A	1	.	I
+chrM	333	T	1	.	I
+chrM	334	A	1	.	I
+chrM	335	C	1	.	I
+chrM	336	G	1	.	I
+chrM	337	A	1	.	I
+chrM	338	T	1	.	I
+chrM	339	T	1	.	I
+chrM	340	A	1	.	I
+chrM	341	A	1	.	D
+chrM	342	C	1	.	I
+chrM	343	C	1	.	I
+chrM	344	C	1	.	I
+chrM	345	A	1	.	I
+chrM	346	A	1	.	;
+chrM	347	A	1	.$	7
+chrM	360	C	1	^:.	I
+chrM	361	G	1	.	I
+chrM	362	G	1	.	I
+chrM	363	C	1	.	I
+chrM	364	G	1	.	I
+chrM	365	T	1	.	I
+chrM	366	A	1	.	I
+chrM	367	A	1	.	I
+chrM	368	A	1	.	I
+chrM	369	G	1	.	I
+chrM	370	C	1	.	I
+chrM	371	G	1	.	I
+chrM	372	T	1	.	I
+chrM	373	G	1	.	I
+chrM	374	T	1	.	I
+chrM	375	C	1	.	I
+chrM	376	A	1	.	I
+chrM	377	A	1	.	I
+chrM	378	A	1	.	I
+chrM	379	G	1	.	I
+chrM	380	A	1	.	I
+chrM	381	C	1	T	I
+chrM	382	T	1	.	I
+chrM	383	A	1	.	I
+chrM	384	A	1	.	I
+chrM	385	T	1	.	I
+chrM	386	A	1	G	I
+chrM	387	C	1	.	I
+chrM	388	C	1	.	I
+chrM	389	A	2	.^:.	II
+chrM	390	A	3	..^:.	III
+chrM	391	A	3	...	>II
+chrM	392	A	3	...	III
+chrM	393	T	3	...	III
+chrM	394	A	3	...	III
+chrM	395	A	3	.$..	III
+chrM	396	A	2	..	II
+chrM	397	G	2	..	II
+chrM	398	T	2	..	EI
+chrM	399	T	2	..	II
+chrM	400	A	3	..^:.	III
+chrM	401	A	3	...	III
+chrM	402	A	3	...	III
+chrM	403	A	3	...	III
+chrM	404	C	3	...	III
+chrM	405	C	3	...	III
+chrM	406	C	3	...	EII
+chrM	407	A	3	...	III
+chrM	408	G	3	...	III
+chrM	409	T	3	...	0II
+chrM	410	T	3	...	III
+chrM	411	A	4	...^:,	IIII
+chrM	412	A	4	...,	FIII
+chrM	413	G	4	...,	IIIH
+chrM	414	C	4	...a	III2
+chrM	415	C	4	TTTt	III7
+chrM	416	G	5	...,^:,	II?7:
+chrM	417	T	5	...,,	;IIE@
+chrM	418	A	5	...,,	IIIII
+chrM	419	A	5	...,,	IIIII
+chrM	420	A	5	...,,	FIIII
+chrM	421	A	5	...,,	IIIII
+chrM	422	A	5	...,,	>IIII
+chrM	423	G	6	...,,^:,	HII/I,
+chrM	424	C	6	.$..a,,	;II-I:
+chrM	425	T	5	.$.,,,	IIIIF
+chrM	426	A	5	.,,,^:,	III@I
+chrM	427	C	5	.,,,,	III$I
+chrM	428	A	5	.,,,,	IIIII
+chrM	429	A	5	.,,,,	IIII.
+chrM	430	C	5	.,,,a	I%I5'
+chrM	431	C	5	.,,,,	I(I5<
+chrM	432	A	5	.,,,,	IIIII
+chrM	433	A	5	.,,,,	0IIII
+chrM	434	A	5	.,,,,	=IIII
+chrM	435	G	5	.$,,,,	EIIII
+chrM	436	T	4	,,,,	III5
+chrM	437	A	4	,,,,	IIII
+chrM	438	A	4	,,,,	IIII
+chrM	439	A	4	,,,,	IIII
+chrM	440	A	4	,,,,	IIIF
+chrM	441	T	6	,,,,^:.^:.	III;II
+chrM	442	A	6	,,,,..	IIIIII
+chrM	443	G	6	,,,,..	IIIIII
+chrM	444	A	6	,,,,..	IIIIII
+chrM	445	C	6	,,,,..	IIIIII
+chrM	446	T	6	,$,,,..	IIIIII
+chrM	447	A	5	,,,..	IIIII
+chrM	448	C	5	,,,..	IIIII
+chrM	449	G	6	,,,..^:,	IIIII6
+chrM	450	A	6	,,,..,	IIIIII
+chrM	451	A	6	,$,,..,	IIIIII
+chrM	452	A	5	,,..,	IIIII
+chrM	453	G	5	,,..,	IIIII
+chrM	454	T	6	,,..,^:,	IIIIII
+chrM	455	G	6	,,..,,	IIIIII
+chrM	456	A	6	,,..,,	IIIIII
+chrM	457	C	6	,,..,,	IIIII=
+chrM	458	T	6	,$,..,,	IIIIII
+chrM	459	T	5	,..,,	IIIII
+chrM	460	T	5	,..,,	IIIII
+chrM	461	A	5	,$..,,	IIIII
+chrM	462	A	4	..,,	IIII
+chrM	463	T	4	..,,	IIIC
+chrM	464	A	4	..,,	IIII
+chrM	465	C	4	..,,	IIII
+chrM	466	C	4	..,,	IIII
+chrM	467	T	4	..,,	II>?
+chrM	468	C	4	..,,	IIII
+chrM	469	T	4	..,,	IIIG
+chrM	470	G	4	..,,	%III
+chrM	471	A	4	..,,	4;II
+chrM	472	C	4	..,,	II3I
+chrM	473	T	4	..,,	IIII
+chrM	474	A	4	..,,	;III
+chrM	475	C	4	..,,	IIII
+chrM	476	A	4	.$.$,,	32II
+chrM	477	C	2	,,	II
+chrM	478	G	2	,,	II
+chrM	479	A	2	,,	II
+chrM	480	T	3	,,^:.	III
+chrM	481	A	3	,,.	III
+chrM	482	G	3	,,.	III
+chrM	483	C	4	,,.^:,	IIIE
+chrM	484	T	4	,$,.,	III9
+chrM	485	A	3	,.,	III
+chrM	486	A	3	,.,	III
+chrM	487	G	3	,.,	III
+chrM	488	A	3	,.,	III
+chrM	489	C	3	,$.,	III
+chrM	490	C	2	.,	II
+chrM	491	C	2	.,	II
+chrM	492	A	2	.,	II
+chrM	493	A	2	.,	II
+chrM	494	A	2	.,	II
+chrM	495	C	2	.,	II
+chrM	496	T	2	.,	I2
+chrM	497	G	2	.,	II
+chrM	498	G	2	.,	II
+chrM	499	G	2	.,	II
+chrM	500	A	2	.,	II
+chrM	501	T	2	.,	II
+chrM	502	T	2	.,	II
+chrM	503	A	2	.,	II
+chrM	504	G	2	.,	II
+chrM	505	A	2	.,	GI
+chrM	506	T	2	.,	II
+chrM	507	A	2	.,	II
+chrM	508	C	2	.,	II
+chrM	509	C	2	.,	II
+chrM	510	C	3	.,^:.	III
+chrM	511	C	3	.,.	III
+chrM	512	A	3	.,.	6II
+chrM	513	C	3	.,.	III
+chrM	514	T	3	.,.	III
+chrM	515	A	3	.$,.	III
+chrM	516	T	2	,.	II
+chrM	517	G	2	,.	II
+chrM	518	C	3	,$.^:.	III
+chrM	519	T	2	..	II
+chrM	520	T	3	..^:,	III
+chrM	521	A	3	..,	III
+chrM	522	G	3	..,	II,
+chrM	523	C	3	..,	III
+chrM	524	C	3	..,	II7
+chrM	525	C	3	..,	III
+chrM	526	T	3	..,	II?
+chrM	527	A	3	..,	III
+chrM	528	A	3	..,	III
+chrM	529	A	3	..,	FII
+chrM	530	C	3	..,	II+
+chrM	531	T	3	..,	III
+chrM	532	A	3	..,	:II
+chrM	533	A	3	..,	DGI
+chrM	534	A	3	..,	III
+chrM	535	A	3	..,	?CI
+chrM	536	T	3	..,	III
+chrM	537	A	3	..,	9II
+chrM	538	G	3	..,	III
+chrM	539	C	3	..,	III
+chrM	540	T	3	..,	III
+chrM	541	T	3	..,	III
+chrM	542	A	4	..,^:.	IIII
+chrM	543	C	4	..,.	IIII
+chrM	544	C	4	..,.	IIII
+chrM	545	A	4	N$.,.	"III
+chrM	546	C	3	.,.	III
+chrM	547	A	3	.,.	DII
+chrM	548	A	3	.,.	EII
+chrM	549	C	3	.,.	III
+chrM	550	A	3	.,.	III
+chrM	551	A	3	.,.	6II
+chrM	552	A	3	.,.	GII
+chrM	553	G	3	.$,.	?II
+chrM	554	C	2	,.	I<
+chrM	555	T	2	,$.	II
+chrM	556	A	2	.^:.	II
+chrM	557	T	2	..	II
+chrM	558	T	2	..	II
+chrM	559	C	2	..	II
+chrM	560	G	2	..	II
+chrM	561	C	2	..	II
+chrM	562	C	2	..	II
+chrM	563	A	2	..	CI
+chrM	564	G	2	..	II
+chrM	565	A	2	..	GI
+chrM	566	G	2	..	II
+chrM	567	T	2	..	/I
+chrM	568	A	2	..	DI
+chrM	569	C	2	..	II
+chrM	570	T	2	..	II
+chrM	571	A	2	..	II
+chrM	572	C	2	..	FI
+chrM	573	T	2	..	9I
+chrM	574	A	2	..	II
+chrM	575	G	2	..	II
+chrM	576	C	2	..	II
+chrM	577	A	3	.$.^:.	III
+chrM	578	A	2	..	II
+chrM	579	C	2	..	II
+chrM	580	A	3	..^:,	III
+chrM	581	G	3	..,	III
+chrM	582	C	3	..,	II?
+chrM	583	C	3	..a	II-
+chrM	584	T	3	..,	IIH
+chrM	585	A	3	..,	III
+chrM	586	A	3	..,	III
+chrM	587	A	4	..,^:,	IIII
+chrM	588	A	4	..,,	IIII
+chrM	589	C	4	..,,	IIII
+chrM	590	T	4	..,,	II.5
+chrM	591	C	4	.$.,,	II<I
+chrM	592	A	3	.,,	III
+chrM	593	A	3	.,,	III
+chrM	594	A	3	.,,	III
+chrM	595	G	3	.,,	III
+chrM	596	G	3	.,,	III
+chrM	597	A	3	.,,	:EI
+chrM	598	C	3	.,,	III
+chrM	599	T	4	.,,^:.	II@I
+chrM	600	T	4	.,,.	IIII
+chrM	601	G	4	.,,.	IIII
+chrM	602	G	4	.,,.	IIII
+chrM	603	C	4	.,,.	IIII
+chrM	604	G	4	.,,.	IIII
+chrM	605	G	4	.,,.	IIII
+chrM	606	T	4	.,,.	5III
+chrM	607	G	4	.,,.	IIII
+chrM	608	C	4	.,,.	*III
+chrM	609	T	5	.,,.^:,	?IIII
+chrM	610	T	5	.,,.,	IIII8
+chrM	611	T	5	.,,.,	IIIII
+chrM	612	A	5	T$,,.,	3IIII
+chrM	613	C	4	,,.,	III)
+chrM	614	A	4	,,.,	IIII
+chrM	615	T	4	,$,.,	IIII
+chrM	616	C	3	,.,	III
+chrM	617	C	3	,.,	III
+chrM	618	C	3	,.,	III
+chrM	619	T	3	,.,	IF9
+chrM	620	C	3	,.,	II7
+chrM	621	T	3	,.,	III
+chrM	622	A	3	,$.,	I7I
+chrM	623	G	2	.,	II
+chrM	624	A	2	.,	9I
+chrM	625	G	2	.,	II
+chrM	626	G	2	.,	II
+chrM	627	A	2	.,	2I
+chrM	628	G	2	.,	II
+chrM	629	C	2	.,	II
+chrM	630	C	2	.,	II
+chrM	631	T	2	.,	II
+chrM	632	G	2	.,	II
+chrM	633	T	2	.,	II
+chrM	634	T	2	.$,	II
+chrM	635	C	1	,	I
+chrM	636	C	1	,	I
+chrM	637	A	1	,	I
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+chrM	639	A	1	,	I
+chrM	640	A	1	,	I
+chrM	641	T	1	,	I
+chrM	642	C	1	,	I
+chrM	643	G	1	,	I
+chrM	644	A	1	,$	I
+chrM	646	A	1	^:.	I
+chrM	647	A	1	.	I
+chrM	648	A	1	.	I
+chrM	649	C	2	.^:,	II
+chrM	650	C	2	.,	II
+chrM	651	C	2	.,	II
+chrM	652	C	3	.,^:,	II)
+chrM	653	G	3	.,,	II2
+chrM	654	A	3	.,,	III
+chrM	655	T	4	.,,^:.	II*I
+chrM	656	A	4	.,,.	IIII
+chrM	657	A	4	.,,.	IIII
+chrM	658	A	4	.,,.	IIII
+chrM	659	C	4	.,,.	IIII
+chrM	660	C	4	.,,.	IIII
+chrM	661	C	4	.,,.	IIII
+chrM	662	C	4	.,,.	IIFI
+chrM	663	A	4	.,,.	=IDI
+chrM	664	C	4	.,,.	II6I
+chrM	665	C	5	.,,.^:,	IIIII
+chrM	666	A	5	.,,.,	BIIII
+chrM	667	T	5	.,,.,	II5I+
+chrM	668	C	5	.,,.,	IIIII
+chrM	669	C	5	.,,.,	IIIII
+chrM	670	C	5	.,a.,	II.II
+chrM	671	T	5	.,,.,	IIIIA
+chrM	672	T	6	.,,.,^:.	FI9I.I
+chrM	673	G	6	.,,.,.	IIIIII
+chrM	674	C	6	.,,.,.	IIIIII
+chrM	675	T	6	.,,.,.	IIIIII
+chrM	676	A	6	.,,.,.	,IIEII
+chrM	677	A	7	.,,.,.^:.	3II;III
+chrM	678	T	7	.,,.,..	IIIIDII
+chrM	679	T	7	.,,.,..	CIIIIII
+chrM	680	C	7	.,,.,..	IIIIIII
+chrM	681	A	7	.$,,.,..	9IIIIII
+chrM	682	G	6	,,.,..	II$III
+chrM	683	C	6	,,.,..	IIIIII
+chrM	684	C	6	,$,.,..	IIIIII
+chrM	685	T	5	,.,..	IIIII
+chrM	686	A	5	,.,..	IIIII
+chrM	687	T	5	,$.,..	IIIII
+chrM	688	A	4	.,..	IIII
+chrM	689	T	4	.,..	IIII
+chrM	690	A	4	.$,..	IIII
+chrM	691	C	3	,..	III
+chrM	692	C	3	,..	III
+chrM	693	G	4	,..^:,	IIII
+chrM	694	C	4	,..,	IIII
+chrM	695	C	4	,..,	IIII
+chrM	696	A	4	,..,	IIII
+chrM	697	T	4	,..,	IIII
+chrM	698	C	4	,..,	IIII
+chrM	699	T	4	,..,	IIII
+chrM	700	T	4	,$..,	IIII
+chrM	701	C	3	..,	III
+chrM	702	A	3	..,	III
+chrM	703	G	3	..,	2II
+chrM	704	C	3	..,	III
+chrM	705	A	3	N.,	"II
+chrM	706	A	3	..,	I5I
+chrM	707	A	3	.$.,	GII
+chrM	708	C	2	.,	II
+chrM	709	C	2	.,	II
+chrM	710	C	2	.,	II
+chrM	711	T	2	.,	II
+chrM	712	A	2	.$,	II
+chrM	713	A	1	,	I
+chrM	714	A	1	,	I
+chrM	715	C	1	,	I
+chrM	716	A	1	,	I
+chrM	717	A	1	,	I
+chrM	718	G	1	,	I
+chrM	719	G	2	,^:,	I&
+chrM	720	T	2	,g	I$
+chrM	721	A	2	,,	I3
+chrM	722	C	2	,,	I$
+chrM	723	C	2	,t	I&
+chrM	724	G	2	,,	I)
+chrM	725	A	2	,,	II
+chrM	726	A	3	,,^:.	III
+chrM	727	G	3	,,.	III
+chrM	728	T	3	,$,.	III
+chrM	729	A	2	,.	II
+chrM	730	A	2	n.	"I
+chrM	731	G	2	,.	II
+chrM	732	C	3	a.^:.	$II
+chrM	733	A	3	,..	III
+chrM	734	C	3	,..	%II
+chrM	735	A	3	,..	III
+chrM	736	A	3	,..	*II
+chrM	737	A	3	,..	III
+chrM	738	T	3	,..	III
+chrM	739	A	3	,..	III
+chrM	740	T	3	,..	III
+chrM	741	C	3	,..	III
+chrM	742	C	3	,..	III
+chrM	743	A	3	,..	III
+chrM	744	A	3	,..	III
+chrM	745	C	3	,..	III
+chrM	746	A	3	,..	IIE
+chrM	747	T	3	,..	III
+chrM	748	A	3	,..	III
+chrM	749	A	3	,..	III
+chrM	750	A	3	,..	III
+chrM	751	A	3	,..	IAI
+chrM	752	A	3	,..	III
+chrM	753	C	3	,..	III
+chrM	754	G	3	,$..	III
+chrM	755	T	2	..	II
+chrM	756	T	3	..^:,	III
+chrM	757	A	3	..,	III
+chrM	758	G	3	..,	III
+chrM	759	G	3	..,	III
+chrM	760	T	3	..,	=II
+chrM	761	C	3	.$.,	IID
+chrM	762	A	2	.,	=I
+chrM	763	A	2	.,	EI
+chrM	764	G	2	.,	II
+chrM	765	G	2	.,	II
+chrM	766	T	2	.,	:I
+chrM	767	G	3	.$,^:,	III
+chrM	768	T	2	,,	I>
+chrM	769	A	3	,,^:,	III
+chrM	770	G	3	,,,	III
+chrM	771	C	3	,,,	IHI
+chrM	772	C	3	,a,	I)/
+chrM	773	C	3	,,,	I7I
+chrM	774	A	4	,,,^:.	II:I
+chrM	775	T	4	,,,.	IH.I
+chrM	776	G	4	,,,.	IIII
+chrM	777	G	4	,,,.	IIII
+chrM	778	G	4	,,,.	IIII
+chrM	779	A	4	,,,.	IIAI
+chrM	780	T	4	,,,.	IIGI
+chrM	781	G	4	,,,.	IIII
+chrM	782	G	4	,,,.	IIII
+chrM	783	A	4	,,,.	IIII
+chrM	784	G	4	,,,.	IIII
+chrM	785	A	4	,,,.	IIII
+chrM	786	G	4	,,,.	IIII
+chrM	787	A	4	,,,.	IIII
+chrM	788	A	4	,,,.	IIII
+chrM	789	A	4	,,,.	IIII
+chrM	790	T	5	,,,.^:.	IIIII
+chrM	791	G	5	,$,,..	IIIII
+chrM	792	G	4	,,..	IIII
+chrM	793	G	4	,,..	IIII
+chrM	794	C	4	,,..	IIII
+chrM	795	T	4	,,..	IIII
+chrM	796	A	4	,,..	IIII
+chrM	797	C	4	,,..	IIII
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+chrM	1092	C	1	n	"
+chrM	1093	A	1	,	I
+chrM	1094	C	1	,	I
+chrM	1095	T	1	,	7
+chrM	1096	C	1	a	B
+chrM	1097	A	1	,	I
+chrM	1098	A	1	,	I
+chrM	1099	A	1	,	I
+chrM	1100	A	1	,	I
+chrM	1101	T	1	,	I
+chrM	1102	G	2	,^:,	(I
+chrM	1103	A	2	,,	II
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+chrM	1105	C	2	,,	.I
+chrM	1106	A	2	,,	8I
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in1.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in1.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM	1	A	G	25	0	25	1	^:.	I
+chrM	2	C	T	25	0	25	2	.N	I$
+chrM	3	T	G	27	0	25	2	..	II
+chrM	4	G	C	36	0	25	3	.^:.^:.	II+
+chrM	5	T	A	38	0	25	3	...	III
+chrM	6	T	A	39	0	25	4	.N..	I$II
+chrM	7	G	C	43	0	25	5	...^:.^:.	IIIII
+chrM	8	A	C	46	0	25	6	.....^:.	IIIIII
+chrM	9	T	G	53	0	25	8	..G...^:.^:.	IIIII$II
+chrM	10	T	G	56	0	25	9	........^:.	IIIIIIIII
+chrM	11	C	G	57	0	25	10	.........^:.	IIIIIIIIII
+chrM	12	T	C	61	0	25	11	..........^:.	IIIIIIIIIII
+chrM	13	T	G	79	0	25	15	.........^:.^:.^:.^:.^:.^:.	IIIIIIIIIIII#II
+chrM	14	A	C	58	0	25	18	.......G.........^:.	BIIIIIII+IIIIIIIII
+chrM	15	G	A	87	0	25	19	..N...............^:.^:.	DIIIIII$(IIIIIIIIIII
+chrM	16	G	C	88	0	25	20	.........N..........	IIIIIIIIIIIIIIIIIIII
+chrM	17	A	C	88	0	25	20	.........G..........	9IIIIIIIIIIIIIIIIIII
+chrM	18	G	A	89	0	25	20	...A................	@IIIIIIIIIIIIIIIIIII
+chrM	19	G	T	58	0	25	20	....T.............GG	IIIIIIIIIIIIIIIIII'A
+chrM	20	T	C	55	0	25	20	.........C........C.	IIIIIIIIIIIIIII2II#$
+chrM	21	C	T	87	0	25	20	..........G.........	IIIIIIIIIIIIIIIIIIII
+chrM	22	C	A	87	0	25	20	..........N.........	IIIIIIIIIIIIIIAIIIII
+chrM	23	A	G	87	0	25	20	.....T..............	9IIIIIIIIII0IIIIIIII
+chrM	24	A	T	89	0	25	20	.....N..N...........	III$IIII"IIIIICII#II
+chrM	25	G	A	57	0	25	21	...A................^:.	A@.$IIIIIIIFIIIIIIIII
+chrM	26	C	G	58	0	25	22	...N....A.............	IIHIDII&IIIIII@IIIIII
+chrM	27	T	A	99	0	25	23	....................^:.^:.^:.	IE8IFIII9IIIIIIIIIIIIII
+chrM	28	A	C	99	0	25	24	..G.....................	1FIIIIIIIIIIIIIIIIDEIIII
+chrM	29	G	C	58	0	25	25	........C.........NN....	;IIIIII+HII=III$III""IIII
+chrM	30	T	T	65	0	25	25	...C....................^:.	;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in2.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in2.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM	1	T	G	25	0	25	1	^:.	I
+chrM	2	C	A	25	0	25	1	.	I
+chrM	3	C	A	25	0	25	2	..	I+
+chrM	4	G	A	36	0	25	3	.^:.^:.	II+
+chrM	5	A	T	36	0	25	3	...	IDI
+chrM	6	A	G	36	0	25	4	..T.	IIBI
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+chrM	8	T	T	45	0	25	6	.....^:.	III$BI
+chrM	9	C	A	51	0	25	8	......^:.^:.	$#III+III
+chrM	10	G	G	54	0	25	9	........^:.	III$III#I
+chrM	11	T	C	57	0	25	10	.........^:.	IIIDBIIIII
+chrM	12	A	T	60	0	25	11	..........^:.	IIIIIIIII$I
+chrM	13	A	T	78	0	25	18	..A.........^:.^:.^:.^:.^:.^:.	III#$IIIIII+IIDIIB
+chrM	14	G	A	56	0	25	19	........T.........^:.	BIIIIIII+IIII$IBIII
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+chr1	2	A	T	87	0	25	20	......G.............	9IIIIIIIIIIIIICBIIII
+chr1	3	A	G	87	0	25	20	....A...............	@IIIIIIIII#IIII#IIII
+chr1	4	A	T	55	0	25	20	..................GG	IIIII@II$IIIIIIIII'A
+chr1	5	C	A	54	0	25	20	.......A..........C.	IIIIIIIIIDIIIII2II#$
+chr1	6	G	T	87	0	25	20	.............A......	IIIIIIIBIIIIII#IIIII
+chr1	7	A	C	87	0	25	20	..........C.........	IIIII+IIIIIIIIAIIIII
+chr1	8	G	A	87	0	25	20	....G.........T.....	9IIIIIIIIII0IIIIIIII
+chr1	9	A	T	87	0	25	20	........N...........	IIII$III"IIIIICIIIII
+chr1	10	G	A	57	0	25	21	...A................^:.	A@.$IIIIIIIFIIIIIIIII
+chr1	11	C	A	57	0	25	22	....G...A.............	IIHIDII&IIIIII#III$II
+chr1	12	T	A	99	0	25	24	.....................^:.^:.^:.	IE8IFIII9IIIIIIIIIIIIIII
+chr1	13	A	C	99	0	25	25	...N.....................	1FIIIIIIIIIIIIIIIIDEII$II
+chr1	14	G	C	55	0	25	25	....G..............NN....	;IIIBIII+HII=IIIIII""IIII
+chr1	15	T	G	68	0	25	28	...C.......N............^:.	;I?&IAI0IIIIIII@II#$II@II
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in3.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in3.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chr1	1	G	G	25	0	25	1	^:.	I
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+chr1	8	T	T	45	0	25	6	.....^:.	IIIIII
+chr1	9	A	A	51	0	25	7	.....^:.^:.	IBIIIII
+chr1	10	G	G	54	0	25	9	........^:.	IIIIIIIII
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+chr4	11	C	C	57	0	25	25	.......A.....GN..........	IIHIDII&III#IIIIIIIIIIIII
+chr4	12	A	A	99	0	25	26	.......................^:.^:.^:.	IE8IFIII9IIIIIII$IIIIIIIII
+chr4	13	A	A	99	0	25	27	........N..................	1FIIIIII$IIIIIIIIIIIIDEIIII
+chr4	14	G	G	55	0	25	28	..N...................NN....	;III$I#IIII+HII=IIIIII""IIII
+chr4	15	G	G	68	0	25	30	...C....N..G.................^:.	;I?&IAI0IIIIIII$#I$@IIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in4.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in4.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr2	1	T	6	.C...,	I$$III
+chr2	2	G	6	..N..,	III@II
+chr2	3	C	7	..C...,	I$IIIII
+chr2	4	G	7	.G....,	I#IIIII
+chr2	5	G	7	...N..,	IIII#BI
+chr2	6	A	7	..T...,	I$IDIII
+chr2	7	T	8	...C...,	IIIBD$II
+chr2	8	A	8	..A....,	IBI#IIII
+chr2	9	C	9	.GA..N..,	I$IBIII#I
+chr2	10	T	9	........,	I$II#IIII
+chr2	11	C	10	.>>..T...,	IIII@I$I$I
+chr2	12	G	10	.N..G....,	III$IIIIII
+chr2	13	A	11	....A..T..,	IIIIII#I@II
+chr1	1	C	1	^:.	I
+chr1	2	G	2	.^:.	$I
+chr1	3	A	2	..	I%
+chr1	4	C	2	..	I$
+chr1	5	T	3	..^:.	I#I
+chr1	6	G	3	..^:,	I#I
+chr1	7	C	4	.N.,	IIII
+chr1	8	A	4	...,	I$II
+chr1	9	T	5	..C.,	I#IDI
+chr1	10	G	5	N...,	IBII@
+chr1	11	A	5	.C..,	I$II#
+chr1	12	C	5	..N.,	I$III
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in5.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in5.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1	42	T	1	^:.	I
+chr1	43	G	2	.^:.	$I
+chr1	44	T	2	..	I%
+chr1	45	C	3	..^:.	III
+chr1	46	G	3	..^:.	I#I
+chr1	47	T	4	...^:,	I#II
+chr1	48	A	4	.N.,	IIII
+chr1	49	C	5	....,	IIIII
+chr1	50	A	5	..G.,	IIIDI
+chr1	51	A	5	A...,	IBIII
+chr1	52	A	5	....,	IIII#
+chr1	53	G	5	..N.,	I$III
+chr2	77	C	6	.G...,	I$$III
+chr2	78	G	6	..N..,	III@II
+chr2	79	T	7	..N...,	I$IIIII
+chr2	80	C	7	.G....,	I#IIIII
+chr2	81	G	7	...A..,	IIII#BI
+chr2	82	A	8	...G...,	I$IDIIII
+chr2	83	A	8	...T...,	IIIBD$II
+chr2	84	T	8	..A....,	IBI#IIII
+chr2	85	G	8	.GA....,	IIBIII#I
+chr2	86	C	9	........,	I$II#IIII
+chr2	87	G	9	....T...,	IIIII$I$I
+chr2	88	G	10	.N..G....,	III$IIIIII
+chr2	89	G	10	...A..T..,	IIIII#I@II
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in6.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in6.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1	42	C	1	^:.	I
+chr1	43	C	2	.^:.	II
+chr1	44	T	2	..	II
+chr1	45	A	3	..^:.	III
+chr1	46	G	4	...^:.	IIII
+chr1	47	A	5	....^:,	IIIII
+chr1	48	T	5	...N,	I#III
+chr1	49	G	5	....,	IIIII
+chr1	50	A	5	.G..,	IIIII
+chr1	51	G	5	....,	IIIII
+chr2	52	T	5	.N..,	II$II
+chr2	53	A	5	....,	IIIII
+chr2	54	T	5	....,	IIIII
+chr2	55	T	5	....,	IIIII
+chr2	56	C	5	....,	IIIBI
+chr2	57	T	5	....,	IDIII
+chr2	58	T	6	.N...,	IIIIII
+chr2	59	A	6	.....,	IIII$I
+chr3	60	C	6	...G.,	I#IIII
+chr3	61	T	6	..N..,	IIIIII
+chr3	62	C	6	...A.,	IIIIII
+chr3	63	C	7	.N....,	IIIIIII
+chr3	64	A	7	...G..,	IIIII$I
+chr3	65	T	7	...AA.,	IIIII@@
+chr3	66	A	7	....N.,	IIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in7.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in7.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,32 @@
+chr2	1	T	6	.C...,	I$$III
+chr2	2	G	6	..N..,	III@II
+chr2	3	C	7	..C...,	I$IIIII
+chr2	4	G	7	.G....,	I#IIIII
+chr2	5	G	7	...N..,	IIII#BI
+chr2	6	A	7	..T...,	I$IDIII
+chr2	7	T	8	...C...,	IIIBD$II
+chr2	8	A	8	..A....,	IBI#IIII
+chr2	9	C	9	.GA..N..,	I$IBIII#I
+chr2	10	T	9	........,	I$II#IIII
+chr2	11	C	10	.>>..T...,	IIII@I$I$I
+chr2	12	G	10	.N..G....,	III$IIIIII
+chr2	13	A	11	....A..T..,	IIIIII#I@II
+chr2	14	G	11	..N.......	IICIBII@AII
+chr2	15	C	11	A.....NG..	IIIIIDIIIII
+chr2	16	T	11	...C.....G	I$IIIB@IIIC
+chr2	17	C	12	G......TN..	IIAII@IIII$I
+chr2	18	A	12	N......G..A	IIIBIII$IIII
+chr2	19	A	13	.......NN...	IIIIIIBIII$$@
+chr2	20	C	13	..GT.......N	IIIIABIIC$III
+chr1	1	C	1	^:.	I
+chr1	2	G	2	.^:.	$I
+chr1	3	A	2	..	I%
+chr1	4	C	2	..	I$
+chr1	5	T	3	..^:.	I#I
+chr1	6	G	3	..^:,	I#I
+chr1	7	C	4	.N.,	IIII
+chr1	8	A	4	...,	I$II
+chr1	9	T	5	..C.,	I#IDI
+chr1	10	G	5	N...,	IBII@
+chr1	11	A	5	.C..,	I$II#
+chr1	12	C	5	..N.,	I$III
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in8.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in8.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,23 @@
+chr1	42	T	1	^:.	I
+chr1	43	G	2	.^:.	$I
+chr1	44	T	2	..	I%
+chr1	45	C	3	..^:.	III
+chr1	46	G	3	..^:.	I#I
+chr1	47	T	4	...^:,	I#II
+chr1	48	A	4	.N.,	IIII
+chr1	49	C	5	....,	IIIII
+chr1	50	A	5	..G.,	IIIDI
+chr1	51	A	5	A...,	IBIII
+chr1	52	A	5	....,	IIII#
+chr1	53	G	5	..N.,	I$III
+chr2	77	C	6	.G...,	I$$III
+chr2	78	G	6	..N..,	III@II
+chr2	79	T	7	..N...,	I$IIIII
+chr2	80	C	7	.G....,	I#IIIII
+chr2	81	G	7	...A..,	IIII#BI
+chr2	82	A	8	...G...,	I$IDIIII
+chr2	83	A	8	...T...,	IIIBD$II
+chr2	84	T	8	..A....,	IBI#IIII
+chr2	85	G	8	.GA....,	IIBIII#I
+chr2	86	C	9	........,	I$II#IIII
+chr2	87	G	9	....T...,	IIIII$I$I
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in9.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in9.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1	43	C	2	.^:.	II
+chr3	65	T	7	...AA.,	IIIII@@
+chr1	44	T	2	..	II
+chr2	54	T	5	....,	IIIII
+chr1	45	A	3	..^:.	III
+chr1	47	A	5	....^:,	IIIII
+chr1	50	A	5	.G..,	IIIII
+chr1	51	G	5	....,	IIIII
+chr2	52	T	5	.N..,	II$II
+chr2	53	A	5	....,	IIIII
+chr3	60	C	6	...G.,	I#IIII
+chr3	61	T	6	..N..,	IIIIII
+chr1	49	G	5	....,	IIIII
+chr2	55	T	5	....,	IIIII
+chr2	56	C	5	....,	IIIBI
+chr2	58	T	6	.N...,	IIIIII
+chr2	59	A	6	.....,	IIII$I
+chr3	62	C	6	...A.,	IIIIII
+chr1	42	C	1	^:.	I
+chr3	63	C	7	.N....,	IIIIIII
+chr1	48	T	5	...N,	I#III
+chr1	46	G	4	...^:.	IIII
+chr3	64	A	7	...G..,	IIIII$I
+chr3	66	A	7	....N.,	IIIIIII
+chr2	57	T	5	....,	IDIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out1.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out1.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,60 @@
+chr1	1					T	T	87	25	G	G	25	25
+chr1	2					A	T	87	25	T	T	25	25
+chr1	3					A	G	87	25	T	T	27	25
+chr1	4					A	T	55	25	A	A	36	25
+chr1	5					C	A	54	25	A	A	36	25
+chr1	6					G	T	87	25	T	T	36	25
+chr1	7					A	C	87	25	G	G	42	25
+chr1	8					G	A	87	25	T	T	45	25
+chr1	9					A	T	87	25	A	A	51	25
+chr1	10					G	A	57	25	G	G	54	25
+chr1	11					C	A	57	25	C	C	57	25
+chr1	12					T	A	99	25	T	T	60	25
+chr1	13					A	C	99	25	T	T	78	25
+chr1	14					G	C	55	25	A	A	56	25
+chr1	15					T	G	68	25	A	A	87	25
+chr4	1									T	T	90	25
+chr4	2									A	A	87	25
+chr4	3									A	A	34	25
+chr4	4									T	T	55	25
+chr4	5									A	A	54	25
+chr4	6									T	T	87	25
+chr4	7									A	A	80	25
+chr4	8									A	A	87	25
+chr4	9									A	A	87	25
+chr4	10									G	G	57	25
+chr4	11									C	C	57	25
+chr4	12									A	A	99	25
+chr4	13									A	A	99	25
+chr4	14									G	G	55	25
+chr4	15									G	G	68	25
+chrM	1	A	G	25	25	T	G	25	25
+chrM	2	C	T	25	25	C	A	25	25
+chrM	3	T	G	27	25	C	A	25	25
+chrM	4	G	C	36	25	G	A	36	25
+chrM	5	T	A	38	25	A	T	36	25
+chrM	6	T	A	39	25	A	G	36	25
+chrM	7	G	C	43	25	C	G	42	25
+chrM	8	A	C	46	25	T	T	45	25
+chrM	9	T	G	53	25	C	A	51	25
+chrM	10	T	G	56	25	G	G	54	25
+chrM	11	C	G	57	25	T	C	57	25
+chrM	12	T	C	61	25	A	T	60	25
+chrM	13	T	G	79	25	A	T	78	25
+chrM	14	A	C	58	25	G	A	56	25
+chrM	15	G	A	87	25	G	A	87	25
+chrM	16	G	C	88	25
+chrM	17	A	C	88	25
+chrM	18	G	A	89	25
+chrM	19	G	T	58	25
+chrM	20	T	C	55	25
+chrM	21	C	T	87	25
+chrM	22	C	A	87	25
+chrM	23	A	G	87	25
+chrM	24	A	T	89	25
+chrM	25	G	A	57	25
+chrM	26	C	G	58	25
+chrM	27	T	A	99	25
+chrM	28	A	C	99	25
+chrM	29	G	C	58	25
+chrM	30	T	T	65	25
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out2.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out2.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,65 @@
+chr1	1	C	1
+chr1	2	G	2
+chr1	3	A	2
+chr1	4	C	2
+chr1	5	T	3
+chr1	6	G	3
+chr1	7	C	4
+chr1	8	A	4
+chr1	9	T	5
+chr1	10	G	5
+chr1	11	A	5
+chr1	12	C	5
+chr1	42			T	1	C	1
+chr1	43			G	2	C	2
+chr1	44			T	2	T	2
+chr1	45			C	3	A	3
+chr1	46			G	3	G	4
+chr1	47			T	4	A	5
+chr1	48			A	4	T	5
+chr1	49			C	5	G	5
+chr1	50			A	5	A	5
+chr1	51			A	5	G	5
+chr1	52			A	5
+chr1	53			G	5
+chr2	1	T	6
+chr2	2	G	6
+chr2	3	C	7
+chr2	4	G	7
+chr2	5	G	7
+chr2	6	A	7
+chr2	7	T	8
+chr2	8	A	8
+chr2	9	C	9
+chr2	10	T	9
+chr2	11	C	10
+chr2	12	G	10
+chr2	13	A	11
+chr2	52					T	5
+chr2	53					A	5
+chr2	54					T	5
+chr2	55					T	5
+chr2	56					C	5
+chr2	57					T	5
+chr2	58					T	6
+chr2	59					A	6
+chr2	77			C	6
+chr2	78			G	6
+chr2	79			T	7
+chr2	80			C	7
+chr2	81			G	7
+chr2	82			A	8
+chr2	83			A	8
+chr2	84			T	8
+chr2	85			G	8
+chr2	86			C	9
+chr2	87			G	9
+chr2	88			G	10
+chr2	89			G	10
+chr3	60					C	6
+chr3	61					T	6
+chr3	62					C	6
+chr3	63					C	7
+chr3	64					A	7
+chr3	65					T	7
+chr3	66					A	7
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out3.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out3.pileup	Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,70 @@
+chr1	1	C	1	^:.
+chr1	2	G	2	.^:.
+chr1	3	A	2	..
+chr1	4	C	2	..
+chr1	5	T	3	..^:.
+chr1	6	G	3	..^:,
+chr1	7	C	4	.N.,
+chr1	8	A	4	...,
+chr1	9	T	5	..C.,
+chr1	10	G	5	N...,
+chr1	11	A	5	.C..,
+chr1	12	C	5	..N.,
+chr1	42				T	1	^:.	C	1	^:.
+chr1	43				G	2	.^:.	C	2	.^:.
+chr1	44				T	2	..	T	2	..
+chr1	45				C	3	..^:.	A	3	..^:.
+chr1	46				G	3	..^:.	G	4	...^:.
+chr1	47				T	4	...^:,	A	5	....^:,
+chr1	48				A	4	.N.,	T	5	...N,
+chr1	49				C	5	....,	G	5	....,
+chr1	50				A	5	..G.,	A	5	.G..,
+chr1	51				A	5	A...,	G	5	....,
+chr1	52				A	5	....,
+chr1	53				G	5	..N.,
+chr2	1	T	6	.C...,
+chr2	2	G	6	..N..,
+chr2	3	C	7	..C...,
+chr2	4	G	7	.G....,
+chr2	5	G	7	...N..,
+chr2	6	A	7	..T...,
+chr2	7	T	8	...C...,
+chr2	8	A	8	..A....,
+chr2	9	C	9	.GA..N..,
+chr2	10	T	9	........,
+chr2	11	C	10	.>>..T...,
+chr2	12	G	10	.N..G....,
+chr2	13	A	11	....A..T..,
+chr2	14	G	11	..N.......
+chr2	15	C	11	A.....NG..
+chr2	16	T	11	...C.....G
+chr2	17	C	12	G......TN..
+chr2	18	A	12	N......G..A
+chr2	19	A	13	.......NN...
+chr2	20	C	13	..GT.......N
+chr2	52							T	5	.N..,
+chr2	53							A	5	....,
+chr2	54							T	5	....,
+chr2	55							T	5	....,
+chr2	56							C	5	....,
+chr2	57							T	5	....,
+chr2	58							T	6	.N...,
+chr2	59							A	6	.....,
+chr2	77				C	6	.G...,
+chr2	78				G	6	..N..,
+chr2	79				T	7	..N...,
+chr2	80				C	7	.G....,
+chr2	81				G	7	...A..,
+chr2	82				A	8	...G...,
+chr2	83				A	8	...T...,
+chr2	84				T	8	..A....,
+chr2	85				G	8	.GA....,
+chr2	86				C	9	........,
+chr2	87				G	9	....T...,
+chr3	60							C	6	...G.,
+chr3	61							T	6	..N..,
+chr3	62							C	6	...A.,
+chr3	63							C	7	.N....,
+chr3	64							A	7	...G..,
+chr3	65							T	7	...AA.,
+chr3	66							A	7	....N.,
diff -r 5f927f52191c -r 3ac95cd927d7 test/functional/test_get_data.py
--- a/test/functional/test_get_data.py	Fri Mar 26 09:51:03 2010 -0400
+++ b/test/functional/test_get_data.py	Fri Mar 26 12:00:55 2010 -0400
@@ -575,5 +575,22 @@
         self.check_history_for_string( 'Pasted Entry' )
         self.check_history_for_string( 'hello world' )
         self.delete_history( id=self.security.encode_id( history.id ) )
+    def test_0165_upload_file( self ):
+        """Test uploading 1.pileup, NOT setting the file format"""
+        self.check_history_for_string( 'Your history is empty' )
+        history = sa_session.query( galaxy.model.History ) \
+                            .filter( and_( galaxy.model.History.table.c.deleted==False,
+                                           galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+                            .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
+                            .first()
+        self.upload_file( '1.pileup' )
+        hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
+                        .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
+                        .first()
+        assert hda is not None, "Problem retrieving hda from database"
+        self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) )
+        self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' )
+        self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' )
+        self.delete_history( id=self.security.encode_id( history.id ) )
     def test_9999_clean_up( self ):
         self.logout()
diff -r 5f927f52191c -r 3ac95cd927d7 tool_conf.xml.sample
--- a/tool_conf.xml.sample	Fri Mar 26 09:51:03 2010 -0400
+++ b/tool_conf.xml.sample	Fri Mar 26 12:00:55 2010 -0400
@@ -61,6 +61,7 @@
     <tool file="filters/compare.xml"/>
     <tool file="new_operations/subtract_query.xml"/>
     <tool file="stats/grouping.xml" />
+    <tool file="new_operations/column_join.xml" />
   </section>
   <section name="Convert Formats" id="convert">
     <tool file="filters/axt_to_concat_fasta.xml" />

    

[galaxy-dev] [hg] galaxy 3565: Added new tabular/pileup join tool and associa...

Greg Von Kuster