- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit a2e4d36c4318: Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288189891 14400 # Node ID a2e4d36c4318bc4ce73af9df869ae4071af33d55 # Parent 0185bb614c7721d6edf6822ad973e589620b91f5 Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh. --- a/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh +++ b/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009 A. Gordon (gordon(a)cshl.edu)

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galaxy-dist commit 6a97d4fc4268: Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288198736 14400 # Node ID 6a97d4fc4268493480a0a3e7462e91f48d926a72 # Parent 121be69ca30675593dc9fc247a4b10a118fed227 Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03. --- a/test-data/gff2bed_out2.bed +++ b/test-data/gff2bed_out2.bed @@ -1,3 +1,3 @@ -chr1 3204562 3661579 Xkr4 0 - 3204562 3204562 0 3 2487,200,947 0,207220,456070 -chr1 4481008 4486494 Sox17 0 - 4481008 4481008 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 -chr1 4763278 4775807 Mrpl15 0 - 4763278 4763278 0 5 3604,124,166,155,154 0,4327,9370,10753,12375 +chr1 3204562 3661579 Xkr4 0 - 3204562 3661579 0 3 2487,200,947 0,207220,456070 +chr1 4481008 4486494 Sox17 0 - 4481008 4486494 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 +chr1 4763278 4775807 Mrpl15 0 - 4763278 4775807 0 5 3604,124,166,155,154 0,4327,9370,10753,12375

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galaxy-dist commit 243d80d9905a: adding setup_rabbitmq.sh script.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288197416 14400 # Node ID 243d80d9905af9121452f1a0955b2b49c076d66e # Parent 9c6040ab75a8397a5708cfec4edfe216927b8220 adding setup_rabbitmq.sh script. web api minor code fixes --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -91,7 +91,10 @@ def submit( api_key, url, data, return_f except urllib2.HTTPError, e: print e print e.read( 1024 ) - sys.exit( 1 ) + if return_formatted: + sys.exit( 1 ) + else: + return 'Error. '+ str( e ) if not return_formatted: return r print 'Response' --- /dev/null +++ b/setup_rabbitmq.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0` +python scripts/galaxy_messaging/server/setup_rabbitmq.py universe_wsgi.ini --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -184,10 +184,11 @@ class DataTransfer(object): url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, self.server_port, api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug(str((self.api_key, url, data))) + log.debug( str( ( self.api_key, url, data ) ) ) retval = api.submit( self.api_key, url, data, return_formatted=False ) - except: - self.error_and_exit(str(e)) + log.debug( str( retval ) ) + except Exception, e: + self.error_and_exit( str( e ) ) def update_status(self, status, dataset_id='All', msg=''): ''' @@ -212,7 +213,7 @@ class DataTransfer(object): api.encode_id( self.config_id_secret, self.request_id ) ) log.debug(str((self.api_key, url, data))) retval = api.update( self.api_key, url, data, return_formatted=False ) - log.debug('done.') + log.debug( str( retval ) ) except urllib2.URLError, e: log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) log.error(traceback.format_exc()) --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -11,13 +11,17 @@ import os, sys, csv, ConfigParser def main( config_file ): - config = ConfigParser.ConfigParser() - config.read( config_file ) - rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) - username = config.get( 'galaxy_amqp', 'userid' ) - password = config.get( 'galaxy_amqp', 'password' ) - virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) - + try: + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + except Exception, e: + print 'Fatal error:', str(e) + sys.exit(1) + cmd_list = [ 'add_user %s %s' % ( username, password ), 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ),

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galaxy-dist commit d57ea326563c: More tweaking to try to get Cuffdiff to pass functional tests. The problem is that Cuffdiff's output is not deterministic, so lines_diff needs to be large enough (but no larger than needed) to accomodate small differences in output.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288216747 14400 # Node ID d57ea326563cb4539e47aae49daa6c5dfc69efc5 # Parent 6a97d4fc4268493480a0a3e7462e91f48d926a72 More tweaking to try to get Cuffdiff to pass functional tests. The problem is that Cuffdiff's output is not deterministic, so lines_diff needs to be large enough (but no larger than needed) to accomodate small differences in output. --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -77,7 +77,7 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/><output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>

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galaxy-dist commit 23844e86e616: Fix error on all uploads < 4b. An exception was raised in the bigwig sniffer, which does a binary unpack.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288376296 14400 # Node ID 23844e86e6167c79737a7e0396c39e350e95d1c4 # Parent 247c19db7f8987d9da245bc750043188d4a7c373 Fix error on all uploads < 4b. An exception was raised in the bigwig sniffer, which does a binary unpack. --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -213,8 +213,11 @@ class BigWig(Binary): def _unpack( self, pattern, handle ): return struct.unpack( pattern, handle.read( struct.calcsize( pattern ) ) ) def sniff( self, filename ): - magic = self._unpack( "I", open( filename ) ) - return magic[0] == self._magic + try: + magic = self._unpack( "I", open( filename ) ) + return magic[0] == self._magic + except: + return False def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "Binary UCSC %s file" % self._name

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galaxy-dist commit 121be69ca306: Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288197699 14400 # Node ID 121be69ca30675593dc9fc247a4b10a118fed227 # Parent 243d80d9905af9121452f1a0955b2b49c076d66e Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test. --- /dev/null +++ b/test-data/cuffdiff_out8.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out9.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out11.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out6.txt @@ -0,0 +1,88 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 +XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 +XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 +XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 +XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 +XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 +XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 +XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 +XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 +XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 +XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 +XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 +XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 +XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 +XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 +XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 +XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 +XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 +XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 +XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 +XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 +XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 +XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 +XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 +XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 +XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 +XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 +XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 +XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 +XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 +XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 +XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 +XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 +XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 +XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 +XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 +XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 +XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 +XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 +XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 +XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 +XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 +XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 +XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 +XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 +XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 +XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 +XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 +XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 +XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 +XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 +XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 +XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 +XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 +XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 +XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 --- /dev/null +++ b/test-data/cuffdiff_out10.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out7.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out1.txt @@ -0,0 +1,99 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes +TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes +TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no +TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes +TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no +TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no +TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no +TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no +TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes +TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes +TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -73,11 +73,21 @@ <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="sPaired" value="single" ftype="sam" /> - -  -  + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="splicing_diff" file="cuffdiff_out9.txt"/> + <output name="promoters_diff" file="cuffdiff_out10.txt"/> + <output name="cds_diff" file="cuffdiff_out11.txt"/></test></tests> --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -111,13 +111,13 @@ def __main__(): shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds_exp.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_promoters.diff" ), options.promoters_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) except Exception, e: stop_err( 'Error in cuffdiff:\n' + str( e ) ) finally: --- /dev/null +++ b/test-data/cuffdiff_out5.txt @@ -0,0 +1,99 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 +TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 +TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 +TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 +TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 +TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 +TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 +TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 +TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 +TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 +TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 +TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 +TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 +TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 +TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 +TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 +TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 +TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 +TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 +TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 +TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 +TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 +TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 +TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 +TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 +TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 --- a/test-data/cuffdiff_out5.tracking +++ /dev/null @@ -1,2 +0,0 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 67745 0 163551 --- /dev/null +++ b/test-data/cuffdiff_out2.txt @@ -0,0 +1,88 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes +XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes +XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes +XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no --- /dev/null +++ b/test-data/cuffdiff_out3.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out4.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant

1 0

galaxy-dist commit 7327a60e3396: pbs_deljob bugfix from Glen Beane.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288287803 14400 # Node ID 7327a60e33968cb067edf6541cc84643f970180d # Parent 0b278c24c19f0a0f7a57b8a33bd6d992461c04c3 pbs_deljob bugfix from Glen Beane. --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -563,7 +563,7 @@ class PBSJobRunner( object ): if c <= 0: log.debug("(%s/%s) Connection to PBS server for job delete failed" % ( job.id, job.job_runner_external_id ) ) return - pbs.pbs_deljob( c, str( job.job_runner_external_id ), 'NULL' ) + pbs.pbs_deljob( c, str( job.job_runner_external_id ), '' ) pbs.pbs_disconnect( c ) log.debug( "(%s/%s) Removed from PBS queue before job completion" % ( job.id, job.job_runner_external_id ) )

1 0

galaxy-dist commit 49c7938d5827: sample tracking web api cleaned up
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288122647 14400 # Node ID 49c7938d582799125a89f0d6ba38be0ddc6f4b4f # Parent d73fa5f14b013333b2e49bfbf775db8dd0197e2b sample tracking web api cleaned up - added a samples controller --- /dev/null +++ b/lib/galaxy/web/api/samples.py @@ -0,0 +1,44 @@ +""" +API operations on a sample tracking system. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +from galaxy.util.bunch import Bunch + +log = logging.getLogger( __name__ ) + +class SamplesController( BaseController ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests/{encoded_request_id}/samples + Displays a collection (list) of sample of a sequencing request. + """ + try: + request_id = trans.security.decode_id( kwd[ 'request_id' ] ) + except TypeError: + trans.response.status = 400 + return "Malformed request id ( %s ) specified, unable to decode." % str( encoded_request_id ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + rval = [] + for sample in request.samples: + item = sample.get_api_value() + item['url'] = url_for( 'samples', + request_id=trans.security.encode_id( request_id ), + id=trans.security.encode_id( sample.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1767,6 +1767,7 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) + api_collection_visible_keys = ( 'id', 'name' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None): self.name = name self.desc = desc @@ -1818,6 +1819,18 @@ class Sample( object ): pexpect.TIMEOUT:print_ticks}, timeout=10) return output.replace(filepath, '').strip() + def get_api_value( self, view='collection' ): + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + except AttributeError: + rval[key] = None + return rval class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None): --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -104,8 +104,15 @@ def app_factory( global_conf, **kwargs ) # If enabled, add the web API if asbool( kwargs.get( 'enable_api', False ) ): add_api_controllers( webapp, app ) - webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'content', + 'contents', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'sample', + 'samples', + path_prefix='/api/requests/:request_id', + parent_resources=dict( member_name='request', collection_name='requests' ) ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -22,23 +22,57 @@ class RequestsController( BaseController GET /api/requests Displays a collection (list) of sequencing requests. """ - query = trans.sa_session.query( trans.app.model.Request )\ - .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ - and trans.app.model.Request.table.c.deleted == False ) ) \ - .all() + # if admin user then return all requests + if trans.user_is_admin(): + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( trans.app.model.Request.table.c.deleted == False )\ + .all() + else: + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ + and trans.app.model.Request.table.c.deleted == False ) ) \ + .all() rval = [] for request in query: item = request.get_api_value() item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) item['id'] = trans.security.encode_id( item['id'] ) + if trans.user_is_admin(): + item['user'] = request.user.email rval.append( item ) return rval - + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/requests/{encoded_request_id} + Displays details of a sequencing request. + """ + try: + request_id = trans.security.decode_id( id ) + except TypeError: + trans.response.status = 400 + return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + item = request.get_api_value() + item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + item['user'] = request.user.email + item['num_of_samples'] = len(request.samples) + return item + @web.expose_api def update( self, trans, id, key, payload, **kwd ): """ PUT /api/requests/{encoded_request_id} - Displays information about a sequencing request. + Updates a request state, sample state or sample dataset transfer status + depending on the update_type """ params = util.Params( kwd ) update_type = None @@ -124,7 +158,3 @@ class RequestsController( BaseController new_status=new_status, error_msg=error_msg ) return status, output - - - -

1 0

galaxy-dist commit e5f90080a2db: Merge with 29157e97e95453c5f9022d9c571527a6de4032e1
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288149696 14400 # Node ID e5f90080a2db9c16bad2300c5ef0b5c49a558638 # Parent 61c786bd2efb6f9cc4d5fa4d43dfb056ed99b909 # Parent 29157e97e95453c5f9022d9c571527a6de4032e1 Merge with 29157e97e95453c5f9022d9c571527a6de4032e1

1 0

galaxy-dist commit 0185bb614c77: Fix condition used to check if tiles have been loaded/drawn in trackster.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288186007 14400 # Node ID 0185bb614c7721d6edf6822ad973e589620b91f5 # Parent e5f90080a2db9c16bad2300c5ef0b5c49a558638 Fix condition used to check if tiles have been loaded/drawn in trackster. --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -772,7 +772,8 @@ var TiledTrack = function() { this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A list of setTimeout() ids used when drawing tiles. + // A list of setTimeout() ids used when drawing tiles. Each ID indicates + // a tile has been requested to be drawn or is being drawn. var draw_tile_ids = {}; while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache @@ -800,8 +801,9 @@ var TiledTrack = function() { // var track = this; var intervalId = setInterval(function() { - if ( draw_tile_ids.length !== 0 ) { - // Add drawing has finished; if there is more than one child in the content div, + // Only do stuff if all tile drawing is complete: + if (obj_length(draw_tile_ids) === 0) { + // All drawing has finished; if there is more than one child in the content div, // remove the first one, which is the oldest. if ( track.content_div.children().length > 1 ) { track.content_div.children( ":first" ).remove(); --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.ti tle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClas s("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.wh ich)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey: this.dbkey}),dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}a.chrom_select.html(h);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var e=0,d=a.tracks.length;e<d;e++){a.tracks[e].is_overview=false}$(this).siblings().filter("canvas").remove(); $(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var i=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(i/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag ",function(i){var f=Math.min(i.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(i.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),i=a.low;a.low=Math.round(f/g*h)+i;a.high=Math.round(d/g*h)+i;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+c ommatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counte r;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max _low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);th is.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b ){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");i f(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200 px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e= b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filterin g_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function( ){if(j.length!==0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.appen d(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache .get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_r ange=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*D ENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>") .attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;thi s.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resol ution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by_tile [a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.left_offse t,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.inc_slot s[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle= "red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G,aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al,S[5][0 ],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av)))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an=0,g=h. length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q},gen_o ptions:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts= a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.ti tle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClas s("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.wh ich)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey: this.dbkey}),dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}a.chrom_select.html(h);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var e=0,d=a.tracks.length;e<d;e++){a.tracks[e].is_overview=false}$(this).siblings().filter("canvas").remove(); $(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var i=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(i/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag ",function(i){var f=Math.min(i.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(i.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),i=a.low;a.low=Math.round(f/g*h)+i;a.high=Math.round(d/g*h)+i;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+c ommatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counte r;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max _low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);th is.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b ){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");i f(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200 px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e= b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filterin g_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function( ){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|H ide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div. append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_ cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.verti cal_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b +1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.colo r;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></inp ut>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px= 0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view. resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by _tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.left_ offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.inc _slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillS tyle="red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G,aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al,S [5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av)))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an=0 ,g=h.length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q}, gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_co unts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

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