galaxy-dev September 2009

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[hg] galaxy 2722: Fixed a bug in fasta_formatter tool test case, ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6ed5f088a2ad changeset: 2722:6ed5f088a2ad user: guru date: Fri Sep 18 15:28:18 2009 -0400 description: Fixed a bug in fasta_formatter tool test case, which was causing the functional tests to fail. 1 file(s) affected in this change: tools/fastx_toolkit/fasta_formatter.xml diffs (12 lines): diff -r bed484895e2d -r 6ed5f088a2ad tools/fastx_toolkit/fasta_formatter.xml --- a/tools/fastx_toolkit/fasta_formatter.xml Fri Sep 18 15:15:39 2009 -0400 +++ b/tools/fastx_toolkit/fasta_formatter.xml Fri Sep 18 15:28:18 2009 -0400 @@ -21,7 +21,7 @@  <param name="input" value="fasta_formatter1.fasta" /> <param name="width" value="0" /> - <output name="output" file="fastx_formatter1.out" /> + <output name="output" file="fasta_formatter1.out" /> </test> <test>

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[hg] galaxy 2721: More work on server side for tracks. Now uses ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bed484895e2d changeset: 2721:bed484895e2d user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 18 15:15:39 2009 -0400 description: More work on server side for tracks. Now uses converters instead of indexers. A wiggle to array_tree converter is provided. Still need to purge indexer stuff. This will not work without new bx egg (or likely at all) 12 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml lib/galaxy/tracks/__init__.py lib/galaxy/tracks/messages.py lib/galaxy/tracks/store.py lib/galaxy/visualization/__init__.py lib/galaxy/visualization/tracks/__init__.py lib/galaxy/visualization/tracks/data/__init__.py lib/galaxy/visualization/tracks/data/array_tree.py lib/galaxy/web/controllers/tracks.py static/scripts/trackster.js diffs (626 lines): diff -r 3f3712d36034 -r bed484895e2d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Fri Sep 18 15:18:57 2009 -0400 +++ b/datatypes_conf.xml.sample Fri Sep 18 15:15:39 2009 -0400 @@ -58,8 +58,9 @@ <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> <datatype extension="txtseq.zip" type="galaxy.datatypes.images:Txtseq" mimetype="application/zip" display_in_upload="true"/> <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> - <indexer file="wiggle.xml" /> + <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/> </datatype> + <datatype extension="array_tree" type="galaxy.datatypes.data:Data" />  <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +from __future__ import division + +import sys + +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.arrays.array_tree import * +from bx.arrays.wiggle import IntervalReader + +def main(): + + input_fname = sys.argv[1] + out_fname = sys.argv[2] + + reader = IntervalReader( open( input_fname ) ) + + # Fill array from wiggle + d = array_tree_dict_from_wiggle_reader( reader, {} ) + + for value in d.itervalues(): + value.root.build_summary() + + f = open( out_fname, "w" ) + FileArrayTreeDict.dict_to_file( d, f ) + f.close() + +if __name__ == "__main__": + main() \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,14 @@ +<tool id="INDEXER_Wiggle_0" name="Index Wiggle for Track Viewer"> +  + <command interpreter="python">wiggle_to_array_tree_converter.py $input $output</command> + <inputs> + <page> + <param format="wiggle" name="input" type="data" label="Choose wiggle"/> + </page> + </inputs> + <outputs> + <data format="array_tree" name="output"/> + </outputs> + <help> + </help> +</tool> \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/tracks/messages.py --- a/lib/galaxy/tracks/messages.py Fri Sep 18 15:18:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -PENDING = "pending" -NO_DATA = "no data" -NO_CHROMOSOME = "no chromosome" -DATA = "data" diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/tracks/store.py --- a/lib/galaxy/tracks/store.py Fri Sep 18 15:18:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -import os -import re -from string import Template -from galaxy.util import sanitize_text - -# extra mappings/escape to keep users from traversing around the -# filesystem and wreaking havoc -extra_mappings = { r"/": "__fs__", r"^manifest.tab$": "__manifest.tab__" } - -def sanitize_name( name ): - name = sanitize_text( name ) - for key, value in extra_mappings.items(): - name = re.sub( key, value, name ) - return name - -class TemplateSubber( object ): - def __init__(self, obj): - self.obj = obj - def get( self, key, default=None ): - return getattr(self.obj, key, default) - def __getitem__(self, key): - return self.get(key) - -class TrackStoreManager( object ): - def __init__(self, path=""): - self.path = path - - def get( self, dataset ): - s = Template(self.path) - return TrackStore( path=s.substitute(TemplateSubber(dataset)) ) - -class TrackStore( object ): - MANIFEST_NAME = "manifest.tab" - - def __init__(self, path=""): - self.path = path - - def get_manifest( self ): - if not self.exists: raise self.DoesNotExist("TrackStore at %s does not exist." % self.path) - manifest_path = os.path.join( self.path, self.MANIFEST_NAME ) - if os.path.exists( manifest_path ): - manifest = {} - for line in open( manifest_path ): - line = line.rstrip("\n\r") - fields = line.split("\t") - manifest[fields[0]] = fields[1:] - return manifest - else: - raise self.DoesNotExist( "Manifest for TrackStore object could not be found." ) - - def get(self, chrom="chr1", resolution=None, **kwargs): - if not self.exists: raise self.DoesNotExist("TrackStore at %s does not exist." % self.path) - object_path = self._get_object_path( chrom, resolution ) - if os.path.exists( object_path ): - return open( object_path, "rb" ) - else: - try: - return kwargs['default'] - except KeyError: - raise self.DoesNotExist("TrackStore object at %s does not exist." % object_path ) - - def set(self, chrom="chr1", resolution=None, data=None): - if not self.exists: self._build_path( self.path ) - if not data: return - object_path = self._get_object_path( chrom, resolution ) - fd = open( object_path, "wb" ) - fd.write( data ) - fd.close() - - def _get_object_path( self, chrom, resolution ): - object_name = sanitize_name(chrom) - if resolution: object_name += "_%d" % resolution - return os.path.join( self.path, object_name ) - - def _build_path( self, path ): - try: - os.mkdir( path ) - except OSError: - self._build_path( os.path.dirname( path ) ) - os.mkdir( path ) - - @property - def exists(self): - return os.path.exists( self.path ) - - class DoesNotExist( Exception ): - pass diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for Galaxy visulization plugins. +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for track style visulization using the trackster UI. +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/data/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/data/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for track data providers +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/data/array_tree.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,50 @@ +""" +Array tree data provider for Galaxy track browser. +""" + +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.arrays.array_tree import FileArrayTreeDict +from math import floor, ceil, log + +# Maybe this should be included in the datatype itself, so users can add their +# own types to the browser as long as they return the right format of data? + +# FIXME: Assuming block size is always 1000 for the moment +BLOCK_SIZE = 1000 + +class ArrayTreeDataProvider( object ): + def __init__( self, dataset ): + self.dataset = dataset + def get_data( self, chrom, start, end ): + start = int( start ) + end = int( end ) + level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 + print "!!!!", start, end, level + # Open the file + print self.dataset.file_name + d = FileArrayTreeDict( open( self.dataset.file_name ) ) + # Get the right chromosome + try: + chrom_array_tree = d[chrom] + except KeyError: + return None + # Is the requested level valid? + assert 0 <= level <= chrom_array_tree.levels + # Calculate the actual start/range/step of the block we're getting + size = BLOCK_SIZE ** (level+1) + block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE + block_step = size // BLOCK_SIZE + indexes = range( block_start, block_start + size, block_step ) + # Return either data point or a summary depending on the level + if level > 0: + s = chrom_array_tree.get_summary( start, level ) + if s is not None: + return zip( indexes, map( float, s.sums / s.counts ) ) + else: + return None + else: + v = chrom_array_tree.get_leaf( start ) + if v is not None: + return zip( indexes, map( float, v ) ) + else: + return None \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Sep 18 15:18:57 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Sep 18 15:15:39 2009 -0400 @@ -9,18 +9,44 @@ Problems -------- - - Assumes that the only indexing type in Galaxy is for this particular - application. Thus, datatypes can only have one indexer, and the presence - of an indexer results in assuming that datatype can be displayed as a track. - + - Only line tracks supported + - Resolutions are a bit wonky + - Must have a LEN file, not currently able to infer from data (not sure we + need to support that, but need to make user defined build support better) """ import math -from galaxy.tracks import messages from galaxy.util.json import to_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson +from galaxy.util.bunch import Bunch + +from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider + +# Message strings returned to browser +messages = Bunch( + PENDING = "pending", + NO_DATA = "no data", + NO_CHROMOSOME = "no chromosome", + DATA = "data" +) + +# Dataset type required for each track type. This needs to be more flexible, +# there might be mutliple types of indexes that suffice for a given track type. +track_type_to_dataset_type = { + "line": "array_tree" +} + +# Mapping from dataset type to a class that can fetch data from a file of that +# type. This also needs to be more flexible. +dataset_type_to_data_provider = { + "array_tree": ArrayTreeDataProvider +} + +# FIXME: hardcoding this for now, but it should be derived from the available +# converters +browsable_types = set( ["wig" ] ) class TracksController( BaseController ): """ @@ -41,24 +67,26 @@ session = trans.sa_session # If the user clicked the submit button explicately, try to build the browser if browse and dataset_ids: + if not isinstance( dataset_ids, list ): + dataset_ids = [ dataset_ids ] dataset_ids = ",".join( map( str, dataset_ids ) ) trans.response.send_redirect( web.url_for( controller='tracks', action='browser', chrom="", dataset_ids=dataset_ids ) ) - return - # Determine the set of all dbkeys that are used in the current history - dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] - dbkey_set = set( dbkeys ) - # If a dbkey argument was not provided, or is no longer valid, default - # to the first one - if dbkey is None or dbkey not in dbkey_set: - dbkey = dbkeys[0] - # Find all datasets in the current history that are of that dbkey and - # have an indexer. - datasets = {} - for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and trans.app.datatypes_registry.get_indexers_by_datatype( dataset.extension ): - datasets[dataset.id] = dataset.name - # Render the template - return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + else: + # Determine the set of all dbkeys that are used in the current history + dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] + dbkey_set = set( dbkeys ) + # If a dbkey argument was not provided, or is no longer valid, default + # to the first one + if dbkey is None or dbkey not in dbkey_set: + dbkey = dbkeys[0] + # Find all datasets in the current history that are of that dbkey + # and can be displayed + datasets = {} + for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): + if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: + datasets[dataset.id] = dataset.name + # Render the template + return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose def browser(self, trans, dataset_ids, chrom=""): @@ -75,13 +103,15 @@ "id": dataset.id } ) dbkey = dataset.dbkey - LEN = self._chroms(trans, dbkey ).get(chrom,0) + chrom_lengths = self._chroms( trans, dbkey ) + if chrom_lengths is None: + error( "No chromosome lengths file found for '%s'" ) return trans.fill_template( 'tracks/browser.mako', dataset_ids=dataset_ids, tracks=tracks, chrom=chrom, dbkey=dbkey, - LEN=LEN ) + LEN=chrom_lengths.get( chrom, 0 ) ) @web.json def chroms(self, trans, dbkey=None ): @@ -91,85 +121,86 @@ """ Called by the browser to get a list of valid chromosomes and lengths """ + # If there is any dataset in the history of extension `len`, this will + # use it db_manifest = trans.db_dataset_for( dbkey ) if not db_manifest: db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) else: db_manifest = db_manifest.file_name manifest = {} - if os.path.exists( db_manifest ): - for line in open( db_manifest ): - if line.startswith("#"): continue - line = line.rstrip("\r\n") - fields = line.split("\t") - manifest[fields[0]] = int(fields[1]) - else: - # try to fake a manifest by reading track stores - datasets = trans.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=trans.history.id).all() - for dataset in datasets: - if not dataset.metadata.dbkey == dbkey: continue - track_store = trans.app.track_store.get( dataset ) - if track_store.exists: - try: - for chrom, fields in track_store.get_manifest().items(): - manifest[chrom] = max(manifest.get(chrom, 0), int(fields[0])) - except track_store.DoesNotExist: - pass + if not os.path.exists( db_manifest ): + return None + for line in open( db_manifest ): + if line.startswith("#"): continue + line = line.rstrip("\r\n") + fields = line.split("\t") + manifest[fields[0]] = int(fields[1]) return manifest - - @web.json - def data( self, trans, dataset_id, chrom="", low="", high="" ): + + @web.json + def data( self, trans, dataset_id, track_type, chrom, low, high ): """ Called by the browser to request a block of data """ + # Load the requested dataset dataset = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) - if not dataset: return messages.NO_DATA + # No dataset for that id + if not dataset: + return messages.NO_DATA + # Dataset is in error state, can't display if dataset.state == trans.app.model.Job.states.ERROR: return messages.NO_DATA - if not dataset.state == trans.app.model.Job.states.OK: + # Dataset is still being generated + if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING - track_store = trans.app.track_store.get( dataset ) - if not track_store.exists: - # Test if we can make a track - indexers = trans.app.datatypes_registry.get_indexers_by_datatype( dataset.extension ) - if indexers: - tool = indexers[0] # They are sorted by class chain so use the top one - # If we can, return pending and launch job - job = trans.app.model.Job() - job.session_id = trans.get_galaxy_session().id - job.history_id = trans.history.id - job.tool_id = tool.id - job.tool_version = "1.0.0" - job.add_input_dataset( "input_dataset", dataset ) - job.add_parameter( "input_dataset", to_json_string( dataset.id ) ) - # This is odd - # job.add_output_dataset( "input_dataset", dataset ) - # create store path, this is rather unclear? - track_store.set() - job.add_parameter( "store_path", to_json_string( track_store.path ) ) - job.flush() - trans.app.job_manager.job_queue.put( job.id, tool ) - return messages.PENDING - else: - return messages.NO_DATA - else: - # Data for that chromosome or resolution does not exist? - # HACK: we're "pending" because the store exists without a manifest - try: - track_store.get_manifest() - except track_store.DoesNotExist: - return messages.PENDING - if chrom and low and high: - low = math.floor(float(low)) - high = math.ceil(float(high)) - resolution = dataset.datatype.get_track_resolution( dataset, low, high ) - try: - data = track_store.get( chrom, resolution ) - except track_store.DoesNotExist: - return messages.NO_DATA - window = dataset.datatype.get_track_window( dataset, data, low, high ) - glob = {"data":window, "type":dataset.datatype.get_track_type()}; - if resolution: glob["resolution"] = resolution - return window - else: - return messages.DATA + # Determine what to return based on the type of track being drawn. + converted_dataset_type = track_type_to_dataset_type[track_type] + converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) + # If at this point we still don't have an `array_tree_dataset`, there + # is now way we can display this data as an array tree + if converted_dataset is None: + return messages.NO_DATA + # Need to check states again for the converted version + if converted_dataset.state == model.Dataset.states.ERROR: + return messages.NO_DATA + if converted_dataset.state != model.Dataset.states.OK: + return messages.PENDING + # We have a dataset in the right format that is ready to use, wrap in + # a data provider that knows how to access it + data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset ) + # Get the requested chunk of data + data = data_provider.get_data( chrom, low, high ) + # Pack into a dictionary and return + return data + + def __dataset_as_type( self, trans, dataset, type ): + """ + Given a dataset, try to find a way to adapt it to a different type. If the + dataset is already of that type it is returned, if it can be converted a + converted dataset (possibly new) is returned, if it cannot be converted, + None is returned. + """ + # Already of correct type + if dataset.extension == type: + return dataset + # See if we can convert the dataset + if type not in dataset.get_converter_types(): + log.debug( "Converstion from '%s' to '%d' not possible", dataset.extension, type ) + return None + # See if converted dataset already exists + converted_datasets = dataset.get_converted_files_by_type( type ) + if converted_datasets: + for d in converted_datasets: + if d and d.state != 'error': + return d + # Conversion is possible but doesn't exist yet, run converter here + # FIXME: this is largely duplicated from DefaultToolAction + assoc = model.ImplicitlyConvertedDatasetAssociation( parent = dataset, file_type = type, metadata_safe = False ) + new_dataset = dataset.datatype.convert_dataset( trans, dataset, type, return_output = True, visible = False ).values()[0] + new_dataset.hid = dataset.hid # Hrrmmm.... + new_dataset.name = dataset.name + new_dataset.flush() + assoc.dataset = new_dataset + assoc.flush() + return new_dataset diff -r 3f3712d36034 -r bed484895e2d static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Sep 18 15:18:57 2009 -0400 +++ b/static/scripts/trackster.js Fri Sep 18 15:15:39 2009 -0400 @@ -1,4 +1,8 @@ var DENSITY = 1000; + +var BLOCK_SIZE = 1000; + +var log = function( x, b ) { return Math.log( x ) / Math.log( b ) } var View = function( chr, length, low, high ) { this.chr = chr; @@ -83,9 +87,12 @@ high = this.view.high, range = high - low; - var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); + var resolution = Math.pow( BLOCK_SIZE, Math.floor( log( range, BLOCK_SIZE ) ) ); + // Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); + + console//.log( "resolution:", resolution ); resolution = Math.max( resolution, 1 ); - resolution = Math.min( resolution, 100000 ); + resolution = Math.min( resolution, 1000000 ); var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -155,7 +162,7 @@ // use closure to preserve this and parameters for getJSON var fetcher = function (ref) { return function () { - $.getJSON( TRACKSTER_DATA_URL + ref.type, { chrom: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) { + $.getJSON( TRACKSTER_DATA_URL, { track_type: ref.type, chrom: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) { if( data == "pending" ) { setTimeout( fetcher, 5000 ); } else { @@ -175,7 +182,7 @@ Track.call( this, name, view, parent_element ); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; - this.cache = new DataCache( "", this, view ); + this.cache = new DataCache( "line", this, view ); }; $.extend( LineTrack.prototype, TiledTrack.prototype, { make_container: function () { @@ -209,35 +216,37 @@ var canvas = element; canvas.get(0).width = canvas.width(); canvas.get(0).height = canvas.height(); - var ctx = canvas.get(0).getContext("2d"); - var in_path = false; - ctx.beginPath(); - var data = chunk.values; - for ( var i = 0; i < data.length - 1; i++ ) { - var x1 = data[i][0] - tile_low; - var y1 = data[i][1]; - var x2 = data[i+1][0] - tile_low; - var y2 = data[i+1][1]; - console.log( x1, y1, x2, y2 ); - // Missing data causes us to stop drawing - if ( isNaN( y1 ) || isNaN( y2 ) ) { - in_path = false; - } else { - // Translate - x1 = x1 * w_scale; - x2 = x2 * w_scale; - y1 = h_scale - y1 * ( h_scale ); - y2 = h_scale - y2 * ( h_scale ); - if ( in_path ) { - ctx.lineTo( x1, y1, x2, y2 ); - } else { - ctx.moveTo( x1, y1, x2, y2 ); - in_path = true; - } - } - } - ctx.stroke(); - return element; + var data = chunk.values; + if ( data ) { + var ctx = canvas.get(0).getContext("2d"); + var in_path = false; + ctx.beginPath(); + // console.log( "Drawing tile" ); + for ( var i = 0; i < data.length - 1; i++ ) { + var x1 = data[i][0] - tile_low; + var y1 = data[i][1]; + var x2 = data[i+1][0] - tile_low; + var y2 = data[i+1][1]; + // Missing data causes us to stop drawing + if ( isNaN( y1 ) || isNaN( y2 ) ) { + in_path = false; + } else { + // Translate + x1 = x1 * w_scale; + x2 = x2 * w_scale; + y1 = h_scale - y1 * ( h_scale ); + y2 = h_scale - y2 * ( h_scale ); + if ( in_path ) { + ctx.lineTo( x1, y1, x2, y2 ); + } else { + ctx.moveTo( x1, y1, x2, y2 ); + in_path = true; + } + } + } + ctx.stroke(); + } + return element; } });

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[hg] galaxy 2720: Galaxy AMQP Listener, first pass
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3f3712d36034 changeset: 2720:3f3712d36034 user: rc date: Fri Sep 18 15:18:57 2009 -0400 description: Galaxy AMQP Listener, first pass Added a check for testing completed requests in Requests functional tests 7 file(s) affected in this change: lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/framework/helpers/grids.py run_galaxy_listener.sh scripts/galaxy_messaging/amqp_consumer.py scripts/galaxy_messaging/galaxydb_interface.py test/functional/test_forms_and_requests.py universe_wsgi.ini.sample diffs (300 lines): diff -r 7f18940a4821 -r 3f3712d36034 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Fri Sep 18 14:21:59 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Sep 18 15:18:57 2009 -0400 @@ -98,7 +98,6 @@ else: self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) - self.__update_request_state(trans) # Render the list view return self.request_grid( trans, **kwargs ) @web.expose @@ -980,12 +979,6 @@ request_id=request.id, msg='Bar codes has been saved for this request', messagetype='done')) - - def __update_request_state(self, trans): - requests = trans.app.model.Request.query.filter_by(deleted=False, - state=trans.app.model.Request.states.SUBMITTED) - for request in requests: - self.__set_request_state(request) def __set_request_state(self, request): # check if all the samples of the current request are in the final state diff -r 7f18940a4821 -r 3f3712d36034 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Fri Sep 18 14:21:59 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Fri Sep 18 15:18:57 2009 -0400 @@ -121,7 +121,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query ): + def apply_default_filter( self, trans, query, **kwargs): return query class GridColumn( object ): diff -r 7f18940a4821 -r 3f3712d36034 run_galaxy_listener.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_galaxy_listener.sh Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,3 @@ +#!/bin/sh + +python scripts/galaxy_messaging/amqp_consumer.py \ No newline at end of file diff -r 7f18940a4821 -r 3f3712d36034 scripts/galaxy_messaging/amqp_consumer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/amqp_consumer.py Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,68 @@ +from amqplib import client_0_8 as amqp +import ConfigParser +import sys +import optparse +import xml.dom.minidom +from galaxydb_interface import GalaxyDbInterface + +galaxy_config_file = 'universe_wsgi.ini' +global dbconnstr + +def get_value(dom, tag_name): + ''' + This method extracts the tag value from the xml message + ''' + nodelist = dom.getElementsByTagName(tag_name)[0].childNodes + rc = "" + for node in nodelist: + if node.nodeType == node.TEXT_NODE: + rc = rc + node.data + return rc + +def recv_callback(msg): + #print 'Received: ' + msg.body + ' from channel #' + str(msg.channel.channel_id) + dom = xml.dom.minidom.parseString(msg.body) + barcode = get_value(dom, 'barcode') + state = get_value(dom, 'state') + print barcode, state + # update the galaxy db + galaxy = GalaxyDbInterface(dbconnstr) + sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode) + if sample_id == -1: + print 'Invalid barcode.' + return + galaxy.change_state(sample_id, state) + +def main(): + config = ConfigParser.ConfigParser() + config.read(galaxy_config_file) + global dbconnstr + dbconnstr = config.get("app:main", "database_connection") + amqp_config = {} + for option in config.options("galaxy:amqp"): + amqp_config[option] = config.get("galaxy:amqp", option) + print amqp_config + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'], + insist=False) + chan = conn.channel() + chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) + chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) + chan.queue_bind(queue=amqp_config['queue'], + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) + + chan.basic_consume(queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, + consumer_tag="testtag") + while True: + chan.wait() + chan.basic_cancel("testtag") + chan.close() + conn.close() + +if __name__ == '__main__': + main() \ No newline at end of file diff -r 7f18940a4821 -r 3f3712d36034 scripts/galaxy_messaging/galaxydb_interface.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/galaxydb_interface.py Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,141 @@ +#/usr/bin/python + +from sqlalchemy import * +from sqlalchemy.orm import sessionmaker +from datetime import datetime, timedelta +import sys +import optparse +import os +import time +import logging + +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'GalaxyDbInterface' ) + +class GalaxyDbInterface(object): + + def __init__(self, dbstr): + self.dbstr = dbstr + self.db_engine = create_engine(self.dbstr) +# self.db_engine.echo = True + self.metadata = MetaData(self.db_engine) + self.session = sessionmaker(bind=self.db_engine) + self.event_table = Table('sample_event', self.metadata, autoload=True ) + self.sample_table = Table('sample', self.metadata, autoload=True ) + self.request_table = Table('request', self.metadata, autoload=True ) + self.state_table = Table('sample_state', self.metadata, autoload=True ) + + def get_sample_id(self, field_name='bar_code', value=None): + if not value: + return -1 + sample_id = -1 + if field_name =='name': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.name==value) + result = stmt.execute() + sample_id = result.fetchone()[0] + elif field_name == 'bar_code': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.bar_code==value) + result = stmt.execute() + x = result.fetchone() + if x: + sample_id = x[0] + log.debug('Sample ID: %i' % sample_id) + return sample_id + log.warning('This sample %s %s does not belong to any sample in the database.' % (field_name, value)) + return -1 + + def current_state(self, sample_id): + ''' + This method returns the current state of the sample for the given sample_id + ''' + stmt = select(columns=[self.event_table.c.sample_state_id], + whereclause=self.event_table.c.sample_id==sample_id, + order_by=self.event_table.c.update_time.desc()) + result = stmt.execute() + all_states = result.fetchall() + current_state_id = all_states[0][0] + return current_state_id + + def all_possible_states(self, sample_id): + subsubquery = select(columns=[self.sample_table.c.request_id], + whereclause=self.sample_table.c.id==sample_id) + self.request_id = subsubquery.execute().fetchall()[0][0] + log.debug('REQUESTID: %i' % self.request_id) + subquery = select(columns=[self.request_table.c.request_type_id], + whereclause=self.request_table.c.id==self.request_id) + request_type_id = subquery.execute().fetchall()[0][0] + log.debug('REQUESTTYPEID: %i' % request_type_id) + query = select(columns=[self.state_table.c.id, self.state_table.c.name], + whereclause=self.state_table.c.request_type_id==request_type_id, + order_by=self.state_table.c.id.asc()) + states = query.execute().fetchall() + log.debug('POSSIBLESTATES: '+ str(states)) + return states + + def change_state(self, sample_id, new_state=None): + ''' + This method changes the state of the sample to the the 'new_state' + ''' + if not new_state: + return + new_state_id = -1 + # find the state_id for this new state in the list of possible states + possible_states = self.all_possible_states(sample_id) + for state_id, state_name in possible_states: + if new_state == state_name: + new_state_id = state_id + if new_state_id == -1: + return + log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) + d = timedelta(hours=4) + i = self.event_table.insert() + i.execute(update_time=datetime.now()+d, + create_time=datetime.now()+d, + sample_id=sample_id, + sample_state_id=int(new_state_id), + comment='bar code scanner') + # if all the samples for this request are in the final state + # then change the request state to 'Complete' + result = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.request_id==self.request_id).execute() + sample_id_list = result.fetchall() + request_complete = True + for sid in sample_id_list: + current_state_id = self.current_state(sid[0]) + if current_state_id != possible_states[-1][0]: + request_complete = False + break + if request_complete: + request_state = 'Complete' + else: + request_state = 'Submitted' + log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) + d = timedelta(hours=4) + i = self.request_table.update(whereclause=self.request_table.c.id==self.request_id, + values={self.request_table.c.state: request_state}) + i.execute() + + + +if __name__ == '__main__': + print '''This file should not be run directly. To start the Galaxy AMQP Listener: + %sh run_galaxy_listener.sh''' +# dbstr = 'postgres://postgres:postgres@localhost/galaxy_ft' +# +# parser = optparse.OptionParser() +# parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ +# action='store', default='bar_code') +# parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ +# action='store') +# parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ +# action='store') +# (opts, args) = parser.parse_args() +# +# gs = GalaxyDbInterface(dbstr) +# sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) +# gs.change_state(sample_id, opts.state) + + + diff -r 7f18940a4821 -r 3f3712d36034 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Sep 18 14:21:59 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Fri Sep 18 15:18:57 2009 -0400 @@ -247,6 +247,8 @@ self.home() request_one.refresh() # check if the request's state is now set to 'complete' + self.visit_url('%s/requests_admin/list?show_filter=Complete' % self.url) + self.check_page_for_string( request_one.name ) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE ) # def test_40_admin_create_request_on_behalf_of_regular_user( self ): # """Testing creating and submitting a request as an admin on behalf of a regular user""" diff -r 7f18940a4821 -r 3f3712d36034 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Fri Sep 18 14:21:59 2009 -0400 +++ b/universe_wsgi.ini.sample Fri Sep 18 15:18:57 2009 -0400 @@ -240,3 +240,22 @@ ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// + + +# Galaxy Message Queue +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +#[galaxy:amqp] +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +

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[hg] galaxy 2718: Unicode support for tags + sqlite
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cbf8667219a4 changeset: 2718:cbf8667219a4 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Sep 18 13:59:50 2009 -0400 description: Unicode support for tags + sqlite 1 file(s) affected in this change: templates/tagging_common.mako diffs (16 lines): diff -r 99b5db852719 -r cbf8667219a4 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Sep 18 13:58:43 2009 -0400 +++ b/templates/tagging_common.mako Fri Sep 18 13:59:50 2009 -0400 @@ -13,7 +13,11 @@ tag_value = "" if tag.value is not None: tag_value = tag.user_value - tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') + ## Tag names and values may be string or unicode object. + if isinstance( tag_name, str ): + tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') + else: ## isInstance( tag_name, unicode ): + tag_names_and_values[tag_name] = tag_value %> // // Returns the number of keys (elements) in an array/dictionary.

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[hg] galaxy 2719: Adding qualsolid_boxplot_graph.sh script used ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7f18940a4821 changeset: 2719:7f18940a4821 user: guru date: Fri Sep 18 14:21:59 2009 -0400 description: Adding qualsolid_boxplot_graph.sh script used by SOLiD quality boxplot tool to the distribution. 2 file(s) affected in this change: tools/solid_tools/qualsolid_boxplot_graph.sh tools/solid_tools/solid_qual_boxplot.xml diffs (110 lines): diff -r cbf8667219a4 -r 7f18940a4821 tools/solid_tools/qualsolid_boxplot_graph.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/solid_tools/qualsolid_boxplot_graph.sh Fri Sep 18 14:21:59 2009 -0400 @@ -0,0 +1,94 @@ +#!/bin/sh + +# Modified fastq_quality_boxplot_graph.sh from FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon(a)cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +function usage() +{ + echo "SOLiD-Quality BoxPlot plotter" + echo "Generates a SOLiD quality score box-plot graph " + echo + echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]" + echo + echo " [-p] - Generate PostScript (.PS) file. Default is PNG image." + echo " [-i INPUT.TXT] - Input file. Should be the output of \"solid_qual_stats\" program." + echo " [-o OUTPUT] - Output file name. default is STDOUT." + echo " [-t TITLE] - Title (usually the solid file name) - will be plotted on the graph." + echo + exit +} + +# +# Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW +# As produced by "solid_qual_stats" program + +TITLE="" # default title is empty +FILENAME="" +OUTPUTTERM="set term png size 800,600" +OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout" +while getopts ":t:i:o:ph" Option + do + case $Option in + # w ) CMD=$OPTARG; FILENAME="PIMSLogList.txt"; TARGET="logfiles"; ;; + t ) TITLE="for $OPTARG" ;; + i ) FILENAME=$OPTARG ;; + o ) OUTPUTFILE="$OPTARG" ;; + p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 4" ;; + h ) usage ;; + * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;; + esac +done +shift $(($OPTIND - 1)) + + +if [ "$FILENAME" == "" ]; then + usage +fi + +if [ ! -r "$FILENAME" ]; then + echo "Error: can't open input file ($1)." >&2 + exit 1 +fi + +#Read number of cycles from the stats file (each line is a cycle, minus the header line) +#But for the graph, I want xrange to reach (num_cycles+1), so I don't subtract 1 now. +NUM_CYCLES=$(cat "$FILENAME" | wc -l) + +GNUPLOTCMD=" +$OUTPUTTERM +set boxwidth 0.8 +set size 1,1 +set key Left inside +set xlabel \"read position\" +set ylabel \"Quality Score \" +set title \"Quality Scores $TITLE\" +#set auto x +set bars 4.0 +set xrange [ 0: $NUM_CYCLES ] +set yrange [-2:45] +set y2range [-2:45] +set xtics 1 +set x2tics 1 +set ytics 2 +set y2tics 2 +set tics out +set grid ytics +set style fill empty +plot '$FILENAME' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \ + '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians' +" + +echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE" diff -r cbf8667219a4 -r 7f18940a4821 tools/solid_tools/solid_qual_boxplot.xml --- a/tools/solid_tools/solid_qual_boxplot.xml Fri Sep 18 13:59:50 2009 -0400 +++ b/tools/solid_tools/solid_qual_boxplot.xml Fri Sep 18 14:21:59 2009 -0400 @@ -1,7 +1,7 @@ <tool id="solid_qual_boxplot" name="Quality Boxplot" version="1.0.0"> <description>for SOLiD data</description> - <command>qualsolid_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> + <command interpreter="bash">qualsolid_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> <inputs> <param format="txt" name="input" type="data" label="Statistics report file (output of 'Quality Statistics for SOLiD data' tool)" />

1 0

[hg] galaxy 2717: Added pileup-to-interval tool to tool_conf.xml...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/99b5db852719 changeset: 2717:99b5db852719 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Sep 18 13:58:43 2009 -0400 description: Added pileup-to-interval tool to tool_conf.xml.sample 1 file(s) affected in this change: tool_conf.xml.sample diffs (11 lines): diff -r 079541496366 -r 99b5db852719 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 13:45:14 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 13:58:43 2009 -0400 @@ -207,6 +207,7 @@ <tool file="samtools/sam_merge.xml" /> <tool file="samtools/sam_pileup.xml" /> <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> </section> <section name="Rg Data" id="rgData1"> <tool file="rgenetics/rgenetics_import.xml"/>

1 0

[hg] galaxy 2716: lastz commented as per Anton's instructions, t...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/079541496366 changeset: 2716:079541496366 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Sep 18 13:45:14 2009 -0400 description: lastz commented as per Anton's instructions, the wrapper and params will be rewritten shortly. 1 file(s) affected in this change: tool_conf.xml.sample diffs (12 lines): diff -r 16993bf0803e -r 079541496366 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 12:11:43 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 13:45:14 2009 -0400 @@ -194,7 +194,7 @@ <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> <section name="NGS: Mapping" id="solexa_tools"> - <tool file="sr_mapping/lastz_wrapper.xml" /> +  <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="sr_mapping/bowtie_wrapper.xml" />

1 0

[hg] galaxy 2715: Added header removal option to BWA wrapper too...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/16993bf0803e changeset: 2715:16993bf0803e user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Sep 18 12:11:43 2009 -0400 description: Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool. 16 file(s) affected in this change: test-data/bwa_wrapper_in0.fastq test-data/bwa_wrapper_out0.sam test-data/bwa_wrapper_out0.tabular test-data/bwa_wrapper_out0b.sam test-data/bwa_wrapper_out0b.tabular test-data/bwa_wrapper_out1.sam test-data/bwa_wrapper_out1.tabular test-data/bwa_wrapper_out2.sam test-data/bwa_wrapper_out2.tabular test-data/bwa_wrapper_out3.sam test-data/bwa_wrapper_out3.tabular test-data/bwa_wrapper_out4.sam test-data/bwa_wrapper_out4.tabular tools/next_gen_conversion/bwa_solid2fastq_modified.pl tools/sr_mapping/bwa_wrapper.py tools/sr_mapping/bwa_wrapper.xml diffs (1125 lines): diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_in0.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in0.fastq Fri Sep 18 12:11:43 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0.sam --- a/test-data/bwa_wrapper_out0.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out0.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,2 +1,1 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0.tabular --- a/test-data/bwa_wrapper_out0.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0b.sam --- a/test-data/bwa_wrapper_out0b.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out0b.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:phiX LN:5386 1831_573_1004 0 phiX 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0b.tabular --- a/test-data/bwa_wrapper_out0b.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 4 * 0 0 * * 0 0 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out1.sam --- a/test-data/bwa_wrapper_out1.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out1.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:PHIX174 LN:5386 1831_573_1004 0 PHIX174 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out1.tabular --- a/test-data/bwa_wrapper_out1.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -1831_573_1004 0 PHIX174 278 25 33M = 278 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -1831_573_1219 16 PHIX174 2202 37 33M = 2202 0 TGCAGTGGAATAGTCAGGTTAAATTTAATGTGA KJOOHX]KAP[]]MBQ\TUFO]QMFGG=CLZ]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1242 0 PHIX174 648 37 33M = 648 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) -1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -1831_573_1448 16 PHIX174 2563 25 33M = 2563 0 CTTCATTGCATTCAGATGGATACATCTGTCAAC :BMPX5.QUW6+R]RIOU]]]]]]]]WCTQS]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1490 0 PHIX174 1767 25 33M = 1767 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' -1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -1831_573_1647 16 PHIX174 1118 37 33M = 1118 0 GACTCCTTCGAGATGGACGCCGTTGGCGCTCTC XSU]YZSLKMZ]Y[]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1684 16 PHIX174 3696 37 33M = 3696 0 AGTGCTGAGGTTGACTTAGTTCATCAGCAAACG ]]]]V]]]]]]]]]]]]]]]]]]]]]U\]][TX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 -1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, -1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -1831_574_109 0 PHIX174 3729 37 33M = 3729 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGC VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_148 16 PHIX174 2369 37 33M = 2369 0 TAGGTTTTCTGCTTAGGAGTTTAATCATGTTTC XOQ[]]]TKWRCLJJZRR][]TWVGVZW]WZTQ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# -1831_574_243 0 PHIX174 2129 37 33M = 2129 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGC ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -1831_574_575 16 PHIX174 4006 37 33M = 4006 0 AATGTCACGCTGATTATTTTGACTTTGAGCGTA TMHGZ]UE<L]]]EM]K"&I]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_592 16 PHIX174 2950 37 33M = 2950 0 GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCA LLVSIV]]ZSPPSWNDIW\VOM[]]QANSCGKI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- -1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -1831_574_734 16 PHIX174 5263 25 33M = 5263 0 GAGAGATGAGATTGAGGCTGGGAAAAGTTACTG P]VXTGPLRN@KE=ALXC7ARL7;>;OKA/!!< XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_824 16 PHIX174 3997 37 33M = 3997 0 ACCCTTCTGAATGTCACGCTGATTATTTTGACT ]\MN]]U?I]]TAN]]ZGK][\RR]T@>M]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ -1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -1831_574_1194 0 PHIX174 1136 37 33M = 1136 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGT \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1204 16 PHIX174 1445 25 33M = 1445 0 CCTAATGAGCTTAATCAAGATGATGCTCGTTAT JGMO%.S]S>EW]V,=Y[]]PCU]]]X]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -1831_574_1591 16 PHIX174 5118 37 33M = 5118 0 AAGCTGTTCAGAATCAGAATGAGCCGCAACTTC MLII]]\K!7]ST][]]]OO]]]]]X]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1624 16 PHIX174 4058 37 33M = 4058 0 TATTGAGGCTTGTGGCATTTCTACTCTTTCTCA ?IM@DV]M?NRTK@JPXS?>ENI;=AML=7=M[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -1831_574_1903 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1961 0 PHIX174 3555 25 33M = 3555 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTT TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_54 16 PHIX174 3587 37 33M = 3587 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCG ]]4/WZUDARYXKAL]]MR]]]]\]]VW]W]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -1831_575_197 16 PHIX174 4861 37 33M = 4861 0 GCTTGCAAAATACGTGGCCTTATGGTTACAGTA G.<]KNV]]RH@AIT]\SP\]]]Y[]]\RS\]P XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. -1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -1831_575_444 16 PHIX174 5098 37 33M = 5098 0 AGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAA ]Y0/[]]MM]]]VT]]]]]]]]QP]]]TS]]][ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -1831_575_569 0 PHIX174 5043 25 33M = 5043 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAA IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_622 0 PHIX174 2485 37 33M = 2485 0 GTTTTACAGACACCTAAAGCTACATCGTCAACG ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -1831_575_663 16 PHIX174 1554 25 33M = 1554 0 CGACTTCTACCACATCTATTGACATTATGGGTC !&V]]NIPV]]YUXWZWTYPW]]]]]ST]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& -1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# -1831_575_938 16 PHIX174 1133 37 33M = 1133 0 GACGCCGTTGGCGCTCTCCGTCTTTCTCCATTG XJFX]]WUY[]RKYXU]]]]]]]]\]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_970 16 PHIX174 232 37 33M = 232 0 GAGGAGAAGTGGCTTAATATGCTTGGCACGTTC Z]]]XU]]]]]]]]]]]]]]]\]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -1831_575_1138 0 PHIX174 1913 37 33M = 1913 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCT VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1157 16 PHIX174 3736 25 33M = 3736 0 AGCGGTATGGCTCTTCTCATATTGGCGCTACTG TX//[\]PQ]]]Z]]]]GN]]O!']]]]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1180 0 PHIX174 4169 37 33M = 4169 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGT ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -1831_575_1302 16 PHIX174 5202 37 33M = 5202 0 CTTACCAAGCTGGGTTACGACGCGACGCCGTTC ?AGG9<JL@57BI,!6828KG54AH<6B>;VYL XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1310 16 PHIX174 1612 37 33M = 1612 0 TACTGACCAAGAACGTGATTACTTCATGCAGCG [M!!N]]]]]]]OX]]]ZKW]]QQ][][RU]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1321 0 PHIX174 2664 37 33M = 2664 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGAC ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1373 16 PHIX174 4221 37 33M = 4221 0 TCTGACGTTCGTGATGAGTTTGTATCTGTTACT WGIZ]OHLR]]QU]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -1831_575_1436 0 PHIX174 3460 37 33M = 3460 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATA []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1442 0 PHIX174 3317 37 33M = 3317 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTC \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -1831_575_1500 16 PHIX174 4269 37 33M = 4269 0 GAATTGGCACAATGCTACAATGTGCTCCCCCAA ]]]LQ]ZZX]]]][[[[][VZ\][[]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1535 16 PHIX174 1225 37 33M = 1225 0 TCACGTTTATGGTGAACAGTGGATTAAGTTCAT Z\]]][Y][]]]]]]]W]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -1831_576_32 16 PHIX174 988 25 33M = 988 0 TTGAGGATAAATTATGTCTAATATTCAAACTGG !6\NX[\]YMP]]YM]]]]]VMPGDW\]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? -1831_576_86 16 PHIX174 2981 37 33M = 2981 0 CATGTCTAAATTGTTTGGAGGCGGTCAAAAAGC JDKTAEKORA;<GOTUPHGVRTZI?BAMUDCKR XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -1831_576_266 16 PHIX174 280 37 33M = 280 0 AGATATGAGTCACATTTTGTTCATGGTAGAGAT E4FXQMCG]]R<FZG5#.Z]SN]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_327 16 PHIX174 4517 37 33M = 4517 0 TACTATTCAGCGTTTGATGAATGCAATGCGACA \[]]]XQ\]]\X]]]]\Y]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( -1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -1831_576_519 16 PHIX174 1625 37 33M = 1625 0 CGTGATTACTTCATGCAGCGTTACCGTGATGTT KMPKLIVPELLS]XRY]]YWV]]NJY]]Y][SZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_603 16 PHIX174 1576 37 33M = 1576 0 CATTATGGGTCTGCAAGCTGCTTATGCTAATTT ZWU]]ZS\]]]TY]]]RQ]]]Y]]]]VZ]]\S] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_655 16 PHIX174 3292 37 33M = 3292 0 TTGCTGCTGCATTTCCTGAGCTTAATGCTTGGG :@O]QV]]]TK]]]73]]]TM]]]QI[]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### -1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* -1831_576_815 0 PHIX174 5186 37 33M = 5186 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTA Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_882 0 PHIX174 5053 37 33M = 5053 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACT Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_898 0 PHIX174 518 37 33M = 518 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTG ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_923 0 PHIX174 1050 37 33M = 1050 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTC MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -1831_576_1131 16 PHIX174 4061 37 33M = 4061 0 TGAGGCTTGTGGCATTTCTACTCTTTCTCAATC WTLN]WUHL]]S<PZQUOYSFZ]][IUXX>>]M XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -1831_576_1289 16 PHIX174 1899 37 33M = 1899 0 TTCAGTACCTTAACGCTAAAGGTGCTTTGACTT NLU]YXTCQ]][JEJMSX]YRU]]][]]]\X]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -1831_576_1367 0 PHIX174 1839 37 33M = 1839 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTC ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1416 0 PHIX174 4522 37 33M = 4522 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -1831_576_1605 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -1831_576_1729 16 PHIX174 5194 37 33M = 5194 0 TAATCCAACTTACCAAGCTGGGTTACGACGCGA ]VDP]]][]]]]]]]]]]]]]]UW]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 -1831_576_1982 16 PHIX174 5024 37 33M = 5024 0 TAACAAAAAGTCAGATATGGACCTTGCTGCTAA TP\NU]]]W[]]]][]]]]]]]]]]]]]VU]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -1831_577_40 0 PHIX174 2772 25 33M = 2772 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGG JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 -1831_577_133 16 PHIX174 1714 37 33M = 1714 0 CATGCGCTCTAATCTCTGGGCATCTGGCTATGA &/BFXKGOZZEPOS]]]]]]PY]RN]YW]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -1831_577_281 16 PHIX174 4577 37 33M = 4577 0 TTTTGACACTCTCACGTTGGCTGACGACCGATT ]]OI]]]]]\ZY]]WTJS]]\[]]]]]]]\]]P XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_288 0 PHIX174 3201 25 33M = 3201 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGAT SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_322 16 PHIX174 458 37 33M = 458 0 TTCTGCCGTTTTGGATTTAACCGAAGATGATTT OIJWXWT]]WACVSEK5:RJSSRSPVZONR[]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_362 0 PHIX174 2153 37 33M = 2153 0 CTTATTCGCCACCATGATTATGACCAGTGTTTC ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_382 16 PHIX174 4686 37 33M = 4686 0 GGTCGCAAGGCTAATGATTCACACGCCGACTGC HMJXWWS<===S]NGHPXOE;GV]O;CTROUWT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_464 0 PHIX174 2126 25 33M = 2126 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATT ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_488 16 PHIX174 4948 37 33M = 4948 0 GGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG ]OTZ]]]]]][V]Z]YW]]]]]][UTT]Q?COU XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -1831_577_545 0 PHIX174 1711 37 33M = 1711 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTA ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_559 0 PHIX174 3840 25 33M = 3840 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAA ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -1831_577_637 0 PHIX174 4247 37 33M = 4247 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -1831_577_692 0 PHIX174 3905 37 33M = 3905 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTC WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out2.sam --- a/test-data/bwa_wrapper_out2.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out2.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:PHIX174 LN:5386 1378_11_329 77 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ 1378_11_329 141 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# 1378_17_1788 77 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out2.tabular --- a/test-data/bwa_wrapper_out2.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -1378_11_329 69 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ -1378_11_329 133 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# -1378_17_1788 69 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### -1378_17_1788 133 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$###### -1378_25_2035 69 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% -1378_25_2035 133 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# -1378_28_770 69 * 0 0 * * 0 0 GGTTGGGAGTTGGCGCGCGTGGTT ###$##%%$####%#%$#%%#($$ -1378_28_770 133 * 0 0 * * 0 0 CTGCTATGCCGGCCGCCTGCCCCT %##(#$$#%$#$%###$%%$##$# -1378_33_1945 69 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG .6;?;55697>8779457986264 -1378_33_1945 133 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG +9;64287788752796/576352 -1378_34_789 69 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#& -1378_34_789 133 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$ -1378_35_263 69 * 0 0 * * 0 0 GGCGGGGGGGGGGGGGGGGGGGGG $%%&,)3/)%$-6'$&5&#$''5. -1378_35_263 133 * 0 0 * * 0 0 GGGCGGGGGGCGGCGGGGGGGGGG ),,#%'$)'-(%&%'%',%%&&(& -1378_43_186 69 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#' -1378_43_186 133 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$# -1378_51_1671 69 * 0 0 * * 0 0 GGTGTTGTTCGGATGTAGCGTGGG ##%$$####$########$##0## -1378_51_1671 133 * 0 0 * * 0 0 TGGGTAGGTGCGGCTCTTGCGGTC ##$#$%###%%#%#$##$$##### -1378_56_324 69 * 0 0 * * 0 0 GCTGGGTGATCTAAGGAATGTAAT #$#####$$$#$$$$##%###*(# -1378_56_324 133 * 0 0 * * 0 0 AGGCTTGGATTGTTGCGCTGACCT /+#**###%%##%#####$$$#$# -1378_56_773 69 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$ -1378_56_773 133 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$ -1378_62_2027 69 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&# -1378_62_2027 133 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'# -1378_62_2029 69 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%# -1378_62_2029 133 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$### -1378_67_1795 69 * 0 0 * * 0 0 CGTGCCAACGACCGTCCTACGGAG @@.?7@@@.@:@A<<>>=>70<@7 -1378_67_1795 133 * 0 0 * * 0 0 TAGTGGGCTAGTCCGGGATCTACC B@C2@@?;-@@1>'A@@91@.@1' -1378_68_466 69 * 0 0 * * 0 0 GTGTCATCTGAGGTAAAGCATTGT /##$09#$#.=$#$76+$%1'### -1378_68_466 133 * 0 0 * * 0 0 GTGATCGTCGGTGCCAGTCCCTGT #(%)+##$#$#%#+$%##$##### -1378_68_1692 69 * 0 0 * * 0 0 TGTTCGATTTAGGTCTTGCCTCGC ###%%$%%##%$#$##$###$$#$ -1378_68_1692 133 * 0 0 * * 0 0 GGTCTTCTGGGCACGGGCCAAGTT ###)%'&%##$###%#######$# -1378_80_664 69 * 0 0 * * 0 0 TGTCTGCGTTGTATCTCTGGTGTA %##%,%$$#&$$###$#$%##'%# -1378_80_664 133 * 0 0 * * 0 0 CTGCTTTGATCCCCGGTGGAGCAC 7#%###$$6#######$##$$$## -1378_85_1786 69 * 0 0 * * 0 0 CCCTAGGAGCGTATACCGGACGAG ,'&/%/@,&1,&'/)&,6&&1)(( -1378_85_1786 133 * 0 0 * * 0 0 ATACTATGTCGATCTGTAAAAAAA )&.)#3%(a)$&%-,2#&+.-%0&./ -1378_86_1011 69 * 0 0 * * 0 0 AGGCGATGGGATATTATTTTACTT :$###)%##$9$###1$$#$2### -1378_86_1011 133 * 0 0 * * 0 0 CTACGTTATTGCTCTGTTTGTCCT ######$%##$$$%###%#$#### -1378_86_1789 69 * 0 0 * * 0 0 GGCCAGGTACTAATAAATTCAACA 1.51/&%#'$,*?%#6&0$$5,20 -1378_86_1789 133 * 0 0 * * 0 0 CGAATATCCCCTGGTTTAGAAGTA 61?1;@/>@<=/(.7'(<5@=%$= -1378_91_1596 69 * 0 0 * * 0 0 GCTTTTTCATTCGGTGCCTTTGGA '>%/3%=()8'#.%?50$&5>%)% -1378_91_1596 133 * 0 0 * * 0 0 TTAGCGGTTGACTATCTGCTGACA *&+'#9'(%*'#//,&<),/)'*# -1378_94_1595 69 * 0 0 * * 0 0 GCGGGTTAACCCAGTACCTCTGGC ,8@6'>8<76>@@(->9)7'*941 -1378_94_1595 133 * 0 0 * * 0 0 CGTGCGACAGCCCATGTTTTCAGA -=..5,3826&*+.+#+#%%6;%# -1378_95_1039 69 * 0 0 * * 0 0 GTTCTGTGCCAGGTGAGGTACGGA &##,./#$&)6##+,'#$$0(##$ -1378_95_1039 133 * 0 0 * * 0 0 CGGCGTCCATCTTCGCCTTGAGAT $##.#$##$$#%$#$%%$###$)$ -1378_95_1767 69 * 0 0 * * 0 0 CTAATTGACCGGGCAAGCTATTAA ',,2'(10/>:=/7).3&%6&)&6 -1378_95_1767 133 * 0 0 * * 0 0 ACACGCACCATCTGGCGGCTAACC 86<65<4<C27/$5+#;-$+#2%$ -1378_96_1037 69 * 0 0 * * 0 0 CTGCTGGGCCATTTGACTTACTCA '$#+#(##-%5##+*&###-.$$$ -1378_96_1037 133 * 0 0 * * 0 0 ATCCCCCAAGATGCCTGTTGATTG $#$'##$$$#%$$#%###+##$#$ -1378_96_1764 69 * 0 0 * * 0 0 TCTTTGTAACCCACTTAGTATTTC 4='28>.@4881B807:822>%)1 -1378_96_1764 133 * 0 0 * * 0 0 TACACCGGAACCTTGCACTAAAGC 6-9'<#+81?+*<8-=69&6;*3) -1378_98_1574 69 * 0 0 * * 0 0 AGGCGAGTGTGGGGGTTGTTTGAG +%%$#)##%##$####%###$%$# -1378_98_1574 133 * 0 0 * * 0 0 GTTCTGCCGGTGTCTGTGGCGGGC $$#+&$$####%$$$###$%#%%# -1378_107_1647 69 * 0 0 * * 0 0 GGTCTGGTTCTATGTTGGTCGACT ###'$$#$$$(#%###(#$##$%# -1378_107_1647 133 * 0 0 * * 0 0 AGGCCTACTACGCGTCATTGATAG &#$$#$(.#%#$$####&$%##($ -1378_111_829 69 * 0 0 * * 0 0 GGTCTTCTATGGTGCTAAATTAGT $##'&###$##)#%($#$%#$'%# -1378_111_829 133 * 0 0 * * 0 0 TGCGGCACTTGCTTCTTCGTATTT %#%##%#$%#$#%###$$##&#$$ -1378_111_1900 69 * 0 0 * * 0 0 GCACGCCTTTGGGCTAAGCCGTAA )$)'#%$########$'#&%$#(# -1378_111_1900 133 * 0 0 * * 0 0 TCCCCTCGCTCGGCTCTGTGCTGT $&%*$#(#)##$#'##%(##$#$% -1378_112_1483 69 * 0 0 * * 0 0 TGGAGTGGTGTGTTTGCTGAGCCA #$#)#############$#%#%'% -1378_112_1483 133 * 0 0 * * 0 0 TGTCCAGCTATGCGGCTTCCTCCT %#$+#%#&#$#####%####%$## -1378_125_1287 69 * 0 0 * * 0 0 TGACGTGGGTTGTCCCGTGAGATT ##$%%#$###$##$$#&%##$(%% -1378_125_1287 133 * 0 0 * * 0 0 TGTCTCTGGGGGGCCTGGTTAGGT $##13$'%#$###$$###$$$#&# -1378_126_468 69 * 0 0 * * 0 0 AAAAAACGGGCCGGGCGGACTAGG @@B@@@>@2>1+?:92)>@8&&<+ -1378_126_468 133 * 0 0 * * 0 0 TCTCCTGATTAGACATATCTCCGT 7>@318?=,=8@49579?..7,7) -1378_127_664 69 * 0 0 * * 0 0 TCGCTTTGCCTATGTTTGTTCGGA #%$%#&##$%#%%###$$###)-' -1378_127_664 133 * 0 0 * * 0 0 AGAGGTTGGTGTCTTGTCGCAGCT ##'#$######$$%######$$$# -1378_129_463 69 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAA ,)&20%8'(&35-***1-2&+510 -1378_129_463 133 * 0 0 * * 0 0 CCTGTGGGCCAAGCCCAATGAAAG 8),,<6(--)<()5&.&/8+;.2+ -1378_129_875 69 * 0 0 * * 0 0 GACCTTTACGTATTGGGGGTTGGC ###)###+###$##$#&%##$,#$ -1378_129_875 133 * 0 0 * * 0 0 TTTCTATGGCTTACGCTGTCTGCC #$($##%####%$#$#####$### -1378_140_1251 69 * 0 0 * * 0 0 TTTCCTTCGTGTGCGTGCGGAGTG #%#%$##$$$######.$$$%#%( -1378_140_1251 133 * 0 0 * * 0 0 ATCCTAGCGCGGTGTCTTGGGGAC #$%1#$$$##$##$#$#$##$%$$ -1378_141_809 69 * 0 0 * * 0 0 TCTCGTGGTTTCTTTTTTATGTGT ##%)##$$#####%$#$#%%#'## -1378_141_809 133 * 0 0 * * 0 0 TGTCCTCCAGTGTCTGTTGGGTGT %&,-##$$#(%###$#$$'###'# -1378_144_983 69 * 0 0 * * 0 0 GTTCGTTCGTGGTGTACGAGGGTG #(#%#####($#%##$$#%##%#) -1378_144_983 133 * 0 0 * * 0 0 AGCGCCCGGTTGGTGCGGCTCGTC -$(&%*$#*#))#$$$#%%$#$## -1378_153_270 69 * 0 0 * * 0 0 GGCCGTGTGCGGGTGTAGATTGGA %$##($######&##$&$$$$%## -1378_153_270 133 * 0 0 * * 0 0 AGTCCTTGTCCCCTGGGTTTTCCC +''$#&%$%#$##&$$($#&#$$# -1378_155_1689 69 * 0 0 * * 0 0 CGCGTTCGGACAAAGCTAGCACCT @4@@=6=@@<4:@@681@@@.24. -1378_155_1689 133 * 0 0 * * 0 0 TTGGGAGGGAGAGAGACTAGACCG ?4@@4<<??<?-@4@=4<5<?:/> -1378_157_1580 69 * 0 0 * * 0 0 GGGATTGAAGGGATGTATGCTAGG #%$&%#$$'%$%#$##*#%$$$$# -1378_157_1580 133 * 0 0 * * 0 0 TGGGCCTCGGTGCCCTTGGTCTGT #%)$##'#$$$&#####%#$#$## -1378_161_317 69 * 0 0 * * 0 0 AATCCATACCCACAAAAGCAGGCC .&%','(@''?7//+&)+2.+)0) -1378_161_317 133 * 0 0 * * 0 0 TTGGCCGGCAACCCCGGTACCTAA 7<,<'@)@>.)2@/')'&(?/-<( -1378_177_735 69 * 0 0 * * 0 0 CGAGCCCTAAACCATGAGATCGGA @@B>@AC9@A<B8@=9>7@5)>,0 -1378_177_735 133 * 0 0 * * 0 0 AGTACGCCATGTATTTGCGACCAG =?@?C<88@=>:7>@55/.,416, -1378_181_1684 69 * 0 0 * * 0 0 TTTCTGTTGTGGTTTTGTTGGGGT $##'$%'##%##$%$#$$####$* -1378_181_1684 133 * 0 0 * * 0 0 CGACTCCCGCATTCACGGTCAAGT &*#,##$#&$*$$#$#$$$#%$## -1378_187_1407 69 * 0 0 * * 0 0 TTGGGTGAAATCTTGTCGAGTGGA ####&##$$###$#####%##%%) -1378_187_1407 133 * 0 0 * * 0 0 TGGCGTCCACTCGTGGGTCTATCG $#$'%#$%$%&$%#####$#$#%# -1378_203_721 69 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/. -1378_203_721 133 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2& -1378_206_2039 69 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05 -1378_206_2039 133 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out3.sam --- a/test-data/bwa_wrapper_out3.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out3.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,2 +1,1 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out3.tabular --- a/test-data/bwa_wrapper_out3.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out4.sam --- a/test-data/bwa_wrapper_out4.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out4.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,3 +1,2 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out4.tabular --- a/test-data/bwa_wrapper_out4.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 76759e07013b -r 16993bf0803e tools/next_gen_conversion/bwa_solid2fastq_modified.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/next_gen_conversion/bwa_solid2fastq_modified.pl Fri Sep 18 12:11:43 2009 -0400 @@ -0,0 +1,112 @@ +#!/usr/bin/perl -w + +# Author: lh3 +# Note: Ideally, this script should be written in C. It is a bit slow at present. + +use strict; +use warnings; +use Getopt::Std; + +my %opts; +my $version = '0.1.2'; +my $usage = qq{ +Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <outfile3> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual> + +Note: <in.title> is the string showed in the `# Title:' line of a + ".csfasta" read file. Then <in.title>F3.csfasta is read sequence + file and <in.title>F3_QV.qual is the quality file. If + <in.title>R3.csfasta is present, this script assumes reads are + paired; otherwise reads will be regarded as single-end. + + The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3 + tag and `2' for F3. Usually you may want to use short <out.prefix> + to save diskspace. Long <out.prefix> also causes troubles to maq. + +}; + +getopts('', \%opts); +die($usage) if (@ARGV != 8); +my ($is_paired,$outfile1,$outfile2,$outfile3,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV; +my (@fhr, @fhw); +my $fn = ''; +my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual); +#my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual'); +#my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0; +if ($is_paired eq "yes") { # paired end + for (0 .. 3) { + $fn = $fn_suff[$_]; + $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz"); + open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n"); + } + open($fhw[0], "|gzip >$outfile2") || die; + open($fhw[1], "|gzip >$outfile1") || die; + open($fhw[2], "|gzip >$outfile3") || die; + my (@df, @dr); + @df = &read1(1); @dr = &read1(2); + while (@df && @dr) { + if ($df[0] eq $dr[0]) { # mate pair + print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1]; + @df = &read1(1); @dr = &read1(2); + } else { + if ($df[0] le $dr[0]) { + print {$fhw[2]} $df[1]; + @df = &read1(1); + } else { + print {$fhw[2]} $dr[1]; + @dr = &read1(2); + } + } + } + if (@df) { + print {$fhw[2]} $df[1]; + while (@df = &read1(1, $fhr[0], $fhr[1])) { + print {$fhw[2]} $df[1]; + } + } + if (@dr) { + print {$fhw[2]} $dr[1]; + while (@dr = &read1(2, $fhr[2], $fhr[3])) { + print {$fhw[2]} $dr[1]; + } + } + close($fhr[$_]) for (0 .. $#fhr); + close($fhw[$_]) for (0 .. $#fhw); +} else { # single end + for (0 .. 1) { + my $fn = "$fn_suff[$_]"; + $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz"); + open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n"); + } + open($fhw[2], "|gzip >$outfile1") || die; + my @df; + while (@df = &read1(1, $fhr[0], $fhr[1])) { + print {$fhw[2]} $df[1]; + } + close($fhr[$_]) for (0 .. $#fhr); + close($fhw[2]); +} + +sub read1 { + my $i = shift(@_); + my $j = ($i-1)<<1; + my ($key, $seq); + my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]); + while (<$fhs>) { + my $t = <$fhq>; + if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) { + $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines + #print $key; + die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t); + my $name = "$1_$2_$3/$i"; + $_ = substr(<$fhs>, 2); + tr/0123./ACGTN/; + my $s = $_; + $_ = <$fhq>; + s/^(\d+)\s*//; + s/(\d+)\s*/chr($1+33)/eg; + $seq = qq/\@$name\n$s+\n$_\n/; + last; + } + } + return defined($seq)? ($key, $seq) : (); +} diff -r 76759e07013b -r 16993bf0803e tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Fri Sep 18 11:11:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Fri Sep 18 12:11:43 2009 -0400 @@ -41,6 +41,7 @@ parser.add_option('', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good') parser.add_option('', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings') parser.add_option('', '--dbkey', dest='dbkey', help='') + parser.add_option('', '--suppressHeader', dest='suppressHeader', help='Suppress header') (options, args) = parser.parse_args() # index if necessary @@ -119,5 +120,29 @@ # clean up temp files tmp_align_out.close() tmp_align_out2.close() + # remove header if necessary + if options.suppressHeader == 'true': + tmp_out = tempfile.NamedTemporaryFile() + cmd4 = 'cp %s %s' % (options.output, tmp_out.name) + try: + os.system(cmd4) + except Exception, erf: + stop_err("Error copying output file before removing headers\n" + str(erf)) + output = file(tmp_out.name, 'r') + fout = file(options.output, 'w') + header = True + line = output.readline() + while line.strip() != '': + if header: + if line.startswith('@HD') or line.startswith('@SQ') or line.startswith('@RG') or line.startswith('@PG') or line.startswith('@CO'): + pass + else: + header = False + fout.write(line) + else: + fout.write(line) + line = output.readline() + fout.close() + tmp_out.close() if __name__=="__main__": __main__() diff -r 76759e07013b -r 16993bf0803e tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Sep 18 11:11:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Sep 18 12:11:43 2009 -0400 @@ -61,6 +61,7 @@ #else: --dbkey="None" #end if + --suppressHeader=$suppressHeader </command> <inputs> <conditional name="solidOrSolexa"> @@ -151,6 +152,7 @@ <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> </when> </conditional> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> </inputs> <outputs> <data format="sam" name="output" /> @@ -163,6 +165,7 @@ <param name="sPaired" value="single" /> <param name="input1" value="bwa_wrapper_in1.fastq" /> <param name="source_select" value="pre_set" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0.sam" ftype="sam" /> </test> <test> @@ -172,6 +175,7 @@ <param name="sPaired" value="single" /> <param name="input1" value="bwa_wrapper_in0.fastq" /> <param name="source_select" value="pre_set" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0b.sam" ftype="sam" /> </test> <test> @@ -198,6 +202,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" /> </test> <test> @@ -225,6 +230,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" /> </test> <test> @@ -251,6 +257,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" /> </test> <test> @@ -278,8 +285,9 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" /> - </test> + </test> </tests> <help>

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[hg] galaxy 2713: getting rid of maq
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5ffb934ab613 changeset: 2713:5ffb934ab613 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 18 10:40:53 2009 -0400 description: getting rid of maq 1 file(s) affected in this change: tool_conf.xml.sample diffs (11 lines): diff -r c1e0a15b5cd5 -r 5ffb934ab613 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 10:29:34 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:40:53 2009 -0400 @@ -192,7 +192,6 @@ <section name="SOLiD: QC" id="solid_tools"> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> - <tool file="solid_tools/maq_cs_wrapper.xml" /> </section> <section name="NGS: Mapping" id="solexa_tools"> <tool file="sr_mapping/lastz_wrapper.xml" />

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[hg] galaxy 2714: small tweaks
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/76759e07013b changeset: 2714:76759e07013b user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 18 11:11:41 2009 -0400 description: small tweaks 2 file(s) affected in this change: tools/metag_tools/split_paired_reads.xml tools/sr_mapping/bowtie_wrapper.xml diffs (26 lines): diff -r 5ffb934ab613 -r 76759e07013b tools/metag_tools/split_paired_reads.xml --- a/tools/metag_tools/split_paired_reads.xml Fri Sep 18 10:40:53 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.xml Fri Sep 18 11:11:41 2009 -0400 @@ -7,8 +7,8 @@ <param name="input" type="data" format="fastqsolexa,fastqsanger" label="Your paired-end file" /> </inputs> <outputs> - <data name="output1" format="fastqsolexa"/> - <data name="output2" format="fastqsolexa"/> + <data name="output1" format="input"/> + <data name="output2" format="input"/> </outputs> <tests> <test> diff -r 5ffb934ab613 -r 76759e07013b tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 18 10:40:53 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 18 11:11:41 2009 -0400 @@ -275,7 +275,7 @@ <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> <conditional name="params"> - <param name="settings_type" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <param name="settings_type" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="pre_set">Commonly used</option> <option value="full">Full parameter list</option> </param>

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galaxy-dev September 2009