Mercurial > repos > yating-l > ucsc_blat
changeset 7:10f3a5b6f2ac draft
planemo upload commit 964ceec6b1c6371b10923c7d49446b1361fc5895-dirty
author | yating-l |
---|---|
date | Mon, 09 Jul 2018 13:07:54 -0400 (2018-07-09) |
parents | 250a7f2b1331 |
children | 7532cec01999 |
files | README.rst blat.xml datatypes_conf.xml test-data/all_fasta.loc test-data/amaVit1_Gallus/Gallus_gallus_RefSeq.fa test-data/amaVit1_Gallus/amaVit1.fa test-data/amaVit1_Gallus/amaVit1_Gallus_gallus.psl test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl test-data/dbia3/dbia3.fa test-data/dbia3/dbia3.sorted.psl test-data/dbia3/dbia3_RM.out test-data/dbia3/dbia3_masked.2bit test-data/dbia3/dbia3_masked.sorted.psl test-data/dbia3/dmel-transcript.fa tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
diffstat | 6 files changed, 260 insertions(+), 310 deletions(-) [+] |
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--- a/blat.xml Thu May 31 11:25:53 2018 -0400 +++ b/blat.xml Mon Jul 09 13:07:54 2018 -0400 @@ -1,70 +1,31 @@ <?xml version="1.0"?> -<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="36"> - <description>BLAST-like sequence alignment tool</description> +<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.1"> + <description>Standalone blat sequence search command line tool</description> <requirements> - <requirement type="package" version="36">blat</requirement> + <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($reference_source.reference_source_selector) == "history": - ## blat depends on file extension - #if $reference_source.database.is_of_type("fasta"): - #set $reference_fasta_filename = "localref.fa" - #elif $reference_source.database.is_of_type("twobit"): - #set $reference_fasta_filename = "localref.2bit" - #else - #set $reference_fasta_filename = "localref" - #end if - + #set $reference_fasta_filename = "localref.fa" ln -s '${reference_source.database}' '${reference_fasta_filename}' && #else: #set $reference_fasta_filename = str($reference_source.database.fields.path) #end if - - blat - + blat + #if $noHead == "yes" + -noHead + #end if -q=$query_type -t=$database_type - - ${oneOff} - - #if str($minScore) - -minScore=${minScore} - #end if - - -maxGap=${maxGap} - - #if str($repMatch) - -repMatch=${repMatch} - #end if - #if $mask_type.mask == "file.out": - -mask='${mask_type.mask_file}' + -mask=$mask_type.mask_file #else: -mask=$mask_type.mask #end if - - #if str($dots) - -dots=${dots} - #end if - - ${trimT} - ${noTrimA} - ${trimHardA} - ${fastMap} - ${fine} - - #if str($maxIntron) - -maxIntron=${maxIntron} - #end if - - ${extendThroughN} - '$reference_fasta_filename' '${query}' - - -out=${out} - - '${output}' + output + && sort -k 10,10 -k 12,12n output > '${output_sorted}' ]]></command> <inputs> <conditional name="reference_source"> @@ -81,10 +42,10 @@ </param> </when> <when value="history"> - <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" /> + <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> </when> </conditional> - <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/> + <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/> <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> <option value="dna">dna - DNA sequence</option> <option value="prot">prot - protein sequence</option> @@ -97,10 +58,10 @@ <option value="dnax">dnax - DNA sequence translated in six frames to protein</option> <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option> </param> - <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" /> - <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" /> - <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" /> - <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" /> + <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." > + <option value="yes" selected="true">Yes, suppresses .psl header</option> + <option value="no">No, do not suppresses .psl header</option> + </param> <conditional name="mask_type"> <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas @@ -115,39 +76,11 @@ <when value="out" /> <when value="file.out"> <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" /> - </when> + </when> </conditional> - <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" /> - <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" /> - <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" /> - <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" /> - <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" /> - <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" /> - <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" /> - <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" /> - <param name="out" type="select" label="Select output file format (-out)"> - <option value="psl">Tab-separated format, no sequence (psl)</option> - <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option> - <option value="axt">Blastz-associated axt format (axt)</option> - <option value="maf">Multiz-associated maf format (maf)</option> - <option value="sim4">Similar to sim4 format (sim4)</option> - <option value="wublast">Similar to WU-BLAST format (wublast)</option> - <option value="blast">Similar to NCBI BLAST format (blast)</option> - <option value="blast8">NCBI BLAST tabular format (blast8)</option> - <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option> - </param> </inputs> <outputs> - <data name="output" format="tabular" label="${tool.name} on ${on_string}"> - <change_format> - <when input="out" value="psl" format="psl" /> - <when input="out" value="axt" format="axt" /> - <when input="out" value="maf" format="maf" /> - <when input="out" value="sim4" format="txt" /> - <when input="out" value="wublast" format="txt" /> - <when input="out" value="blast" format="txt" /> - </change_format> - </data> + <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata --> @@ -155,53 +88,44 @@ <param name="reference_source_selector" value="history" /> <param name="database" value="amaVit1_Gallus/amaVit1.fa" /> <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="lower" /> - <param name="out" value="psl -noHead" /> - <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="True"/> + <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" /> </test> <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome --> <test> <param name="reference_source_selector" value="history" /> <param name="database" value="dbia3/dbia3.fa" /> <param name="query" value="dbia3/dmel-transcript.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="lower" /> - <param name="out" value="psl -noHead" /> - <param name="maxIntron" value="" /> - <output name="output" value="dbia3/dbia3.sorted.psl" sort="True"/> + <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> </test> <!-- test on the database masked by repeat masker --> <test> <param name="reference_source_selector" value="history" /> <param name="database" value="dbia3/dbia3_masked.2bit" /> <param name="query" value="dbia3/dmel-transcript.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> - <param name="oneOff" value="false" /> - <param name="minScore" value="30" /> - <param name="maxGap" value="2" /> - <param name="trimT" value="false" /> - <param name="noTrimA" value="false" /> - <param name="fine" value="false" /> - <param name="maxIntron" value="750000" /> - <param name="extendThroughN" value="false" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="file.out" /> <param name="mask_file" value="dbia3/dbia3_RM.out" /> - <param name="out" value="psl -noHead" /> - <output name="output" value="dbia3/dbia3_masked.sorted.psl"/> + <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" /> </test> - </tests> + </tests> <help> <![CDATA[ BLAT ==== -BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. +BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. -blat (version: v36)- Standalone blat sequence search command line tool. +blat (version: v340)- Standalone blat sequence search command line tool. ------------------------------------------------------------------------- usage: @@ -215,20 +139,25 @@ -ooc=11.ooc tells the program to load over-occurring 11-mers from an external file. This will increase the speed by a factor of 40 in many cases, but is not required. - output.psl is the name of the output file. + output.psl is the name of the output file. documentation: ++++++++++++++ -See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) +See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) Source code: ++++++++++++ http://hgdownload.cse.ucsc.edu/admin/exe/ -]]></help> +]]></help> <citations> <citation type="doi">10.1101/gr.229202</citation> -</citations> +</citations> </tool> + + + + + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Jul 09 13:07:54 2018 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="psl" subclass="True" type="galaxy.datatypes.tabular:Tabular" /> + </registration> +</datatypes> \ No newline at end of file
--- a/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl Thu May 31 11:25:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -1247 370 0 44 6 280 17 96639 +- NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139, 121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923, 9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373, -143 58 0 19 3 659 4 9089 ++ NM_204766 5992 574 1453 LMAW01000003.1 4188689 259524 268833 5 27,80,11,66,36, 574,700,780,847,1417, 259524,261255,261529,262379,268797, -182 48 0 20 1 24 0 0 +- NM_001292086 6644 508 782 LMAW01000003.1 4188689 2832901 2833151 2 102,148, 508,634, 1355538,1355640, -189 73 0 0 4 773 4 13674 ++ NM_204766 5992 553 1588 LMAW01000003.1 4188689 2559457 2573393 5 84,66,33,13,66, 553,739,844,1457,1522, 2559457,2563244,2563349,2570767,2573327, -200 50 0 0 0 0 1 24 +- NM_001292086 6644 481 731 LMAW01000003.1 4188689 2832850 2833124 2 110,140, 481,591, 1355565,1355699, -2134 377 0 62 6 361 28 33978 ++ NM_001006176 3248 296 3230 LMAW01000001.1 10443977 10027590 10064141 29 110,48,10,76,75,152,66,51,87,83,55,56,148,96,63,24,177,107,83,145,109,83,145,90,117,129,68,93,27, 296,406,454,502,578,653,844,910,961,1048,1131,1186,1242,1390,1486,1609,1741,1918,2025,2108,2253,2362,2445,2590,2680,2797,2926,3034,3203, 10027590,10031154,10031353,10031517,10033261,10033696,10034454,10035646,10043484,10043794,10059668,10059824,10059973,10060798,10060979,10061265,10061487,10061740,10061947,10062143,10062365,10062584,10062743,10063001,10063188,10063383,10063616,10063806,10064114, -2710 404 0 198 24 2053 34 11593 +- NM_001292086 6644 10 5375 LMAW01000003.1 4188689 2820233 2835138 37 64,727,107,5,90,146,87,93,135,137,171,93,72,90,69,90,23,34,9,72,125,70,106,21,23,161,26,29,93,15,45,18,11,12,54,162,27, 10,74,801,908,913,1003,1149,1236,1329,1464,1617,1792,1885,2049,2163,2350,2918,3036,3070,3366,3445,3576,3647,3794,3985,4008,4236,4263,4476,4603,4688,4742,4882,4941,5031,5113,5348, 1353551,1355131,1356116,1356798,1356971,1357445,1359020,1359444,1359816,1360523,1360971,1361443,1365082,1365245,1365351,1365525,1366096,1366220,1366255,1366474,1366549,1366674,1366749,1366889,1367081,1367105,1367332,1367358,1367558,1367688,1367786,1367837,1367979,1368029,1368113,1368194,1368429, -3724 1107 0 326 14 609 44 22663 ++ NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, -420 114 0 0 4 99 3 7093 ++ NM_001031013 971 69 702 LMAW01000002.1 5883884 3610886 3618513 5 33,66,21,276,138, 69,138,232,285,564, 3610886,3610955,3617941,3618099,3618375, -49 11 0 0 0 0 0 0 +- NM_001292086 6644 619 679 LMAW01000003.1 4188689 2833085 2833145 1 60, 619, 1355544, -537 234 0 42 7 1113 7 34987 ++ NM_204766 5992 262 2188 LMAW01000001.1 10443977 9729332 9765132 8 108,153,66,93,39,171,99,84, 262,388,574,688,1414,1459,1981,2104, 9729332,9734141,9751019,9755220,9762042,9762555,9764665,9765048, -92 25 0 0 0 0 1 183 +- NM_001292086 6644 562 679 LMAW01000003.1 4188689 2832851 2833151 2 43,74, 562,605, 1355538,1355764,
--- a/test-data/dbia3/dbia3.sorted.psl Thu May 31 11:25:53 2018 -0400 +++ b/test-data/dbia3/dbia3.sorted.psl Mon Jul 09 13:07:54 2018 -0400 @@ -1,147 +1,147 @@ 46 8 0 0 0 0 0 0 ++ FBtr0070000 3537 2966 3020 contig55 40015 26192 26246 1 54, 2966, 26192, -46 8 0 0 0 0 0 0 ++ FBtr0307554 3546 2975 3029 contig55 40015 26192 26246 1 54, 2975, 26192, -46 8 0 0 0 0 0 0 ++ FBtr0307555 4528 3113 3167 contig55 40015 26192 26246 1 54, 3113, 26192, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig65 45013 12112 12160 1 48, 1838, 12112, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig64 40016 32121 32169 1 48, 1838, 32121, +50 10 0 0 0 0 0 0 +- FBtr0070075 2430 1826 1886 contig67 44531 31857 31917 1 60, 1826, 12614, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig10 43013 28990 29035 1 45, 1838, 13978, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig11 35013 7985 8030 1 45, 1838, 26983, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig23 50012 49307 49352 1 45, 1838, 660, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig24 40010 29304 29349 1 45, 1838, 10661, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig25 75023 20928 20973 1 45, 1838, 54050, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig30 70018 55814 55859 1 45, 1838, 14159, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig31 40012 15807 15852 1 45, 1838, 24160, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig35 48011 33007 33052 1 45, 1838, 14959, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig36 45010 8000 8045 1 45, 1838, 36965, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig50 40009 19266 19311 1 45, 1838, 20698, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig51 50015 4265 4310 1 45, 1838, 45705, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig12 56019 44985 45033 1 48, 1838, 44985, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig13 45015 38726 38774 1 48, 1838, 6241, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig14 45010 23718 23766 1 48, 1838, 21244, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51622 51670 1 48, 1838, 51622, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1607 1655 1 48, 1838, 1607, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 36129 36177 1 48, 1838, 36129, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig32 40014 25955 26003 1 48, 1838, 14011, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig33 40016 10953 11001 1 48, 1838, 29015, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig3 40006 37781 37829 1 48, 1838, 2177, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig40 60015 52947 52995 1 48, 1838, 52947, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig41 60014 22938 22986 1 48, 1838, 22938, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig4 55011 27779 27827 1 48, 1838, 27184, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig5 50018 2777 2825 1 48, 1838, 47193, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig58 50011 32281 32329 1 48, 1838, 17682, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig59 40011 22281 22329 1 48, 1838, 17682, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 16718 16766 1 48, 1838, 33247, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 1713 1761 1 48, 1838, 38247, 39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig63 55021 47126 47174 1 48, 1838, 47126, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig60 50013 43000 43048 1 48, 1838, 43000, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 8386 8434 1 48, 1838, 8386, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 7523 7571 1 48, 1838, 7523, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 1858 1906 1 48, 1838, 1858, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 29934 29982 1 48, 1838, 29934, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 28391 28439 1 48, 1838, 28391, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 27528 27576 1 48, 1838, 27528, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 21863 21911 1 48, 1838, 21863, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 5360 5408 1 48, 1838, 5360, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 49939 49987 1 48, 1838, 49939, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 25367 25415 1 48, 1838, 25367, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 1146 1194 1 48, 1838, 1146, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig51 50015 31154 31202 1 48, 1838, 31154, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig50 40009 30606 30654 1 48, 1838, 30606, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig46 50012 1725 1773 1 48, 1838, 1725, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig45 50013 26731 26779 1 48, 1838, 26731, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig45 50013 20131 20179 1 48, 1838, 20131, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig44 50013 36735 36783 1 48, 1838, 36735, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig44 50013 30135 30183 1 48, 1838, 30135, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig41 60014 22938 22986 1 48, 1838, 22938, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig40 60015 52947 52995 1 48, 1838, 52947, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig6 40015 23282 23330 1 48, 1838, 16685, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig64 40016 32121 32169 1 48, 1838, 32121, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig65 45013 12112 12160 1 48, 1838, 12112, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig7 50017 13278 13326 1 48, 1838, 36691, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig13 45015 37571 37619 1 48, 1838, 37571, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig14 45010 22563 22611 1 48, 1838, 22563, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig1 45179 38775 38823 1 48, 1838, 38775, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig24 40010 39021 39069 1 48, 1838, 39021, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig2 45017 23608 23656 1 48, 1838, 23608, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig25 75023 42521 42569 1 48, 1838, 32454, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 48196 48244 1 48, 1838, 48196, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51865 51913 1 48, 1838, 51865, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 9012 9060 1 48, 1838, 9012, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1850 1898 1 48, 1838, 1850, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 63300 63348 1 48, 1838, 63300, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 23293 23341 1 48, 1838, 23293, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig38 50017 35343 35391 1 48, 1838, 35343, 40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig39 45019 20340 20388 1 48, 1838, 20340, 40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig39 45019 7999 8047 1 48, 1838, 7999, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig38 50017 35343 35391 1 48, 1838, 35343, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig32 40014 2484 2532 1 48, 1838, 2484, -42 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1889 contig32 40014 8720 8771 1 51, 1838, 8720, -42 6 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 15422 15470 1 48, 1838, 15422, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 32495 32543 1 48, 1838, 32495, -42 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1889 contig31 40012 38731 38782 1 51, 1838, 38731, -58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig31 40012 1075 1909 2 48,21, 1838,2078, 1075,1888, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 23293 23341 1 48, 1838, 23293, -42 6 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 55429 55477 1 48, 1838, 55429, -58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig30 70018 41082 41916 2 48,21, 1838,2078, 41082,41895, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 63300 63348 1 48, 1838, 63300, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 36129 36177 1 48, 1838, 36129, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1850 1898 1 48, 1838, 1850, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1607 1655 1 48, 1838, 1607, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig44 50013 30135 30183 1 48, 1838, 30135, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig45 50013 20131 20179 1 48, 1838, 20131, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig50 40009 30606 30654 1 48, 1838, 30606, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig51 50015 31154 31202 1 48, 1838, 31154, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 1146 1194 1 48, 1838, 1146, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 49939 49987 1 48, 1838, 49939, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 29934 29982 1 48, 1838, 29934, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig55 40015 14474 14522 1 48, 1838, 25493, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 38030 38078 1 48, 1838, 11935, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig60 50013 43000 43048 1 48, 1838, 43000, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 23025 23073 1 48, 1838, 16935, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig62 50017 34978 35026 1 48, 1838, 14991, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig63 55021 21230 21278 1 48, 1838, 33743, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig64 40016 6225 6273 1 48, 1838, 33743, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig66 45011 6949 6997 1 48, 1838, 38014, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig69 44962 32006 32054 1 48, 1838, 12908, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig70 55020 2053 2101 1 48, 1838, 52919, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig9 60018 37825 37873 1 48, 1838, 22145, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig1 45179 29774 29822 1 48, 1838, 15357, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig15 50014 19711 19759 1 48, 1838, 30255, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig2 45017 14607 14655 1 48, 1838, 30362, 41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 61212 61260 1 48, 1838, 61212, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51865 51913 1 48, 1838, 51865, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 48196 48244 1 48, 1838, 48196, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 9012 9060 1 48, 1838, 9012, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51622 51670 1 48, 1838, 51622, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig24 40010 39021 39069 1 48, 1838, 39021, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig2 45017 23608 23656 1 48, 1838, 23608, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig14 45010 22563 22611 1 48, 1838, 22563, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig13 45015 37571 37619 1 48, 1838, 37571, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig12 56019 44985 45033 1 48, 1838, 44985, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig1 45179 38775 38823 1 48, 1838, 38775, -38 7 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig60 50013 39781 39826 1 45, 2798, 39781, -72 18 0 0 1 231 1 292 ++ FBtr0300326 4823 2538 2859 contig58 50011 15076 15458 2 27,63, 2538,2796, 15076,15395, -50 13 0 0 0 0 0 0 ++ FBtr0300326 4823 2796 2859 contig57 60013 40402 40465 1 63, 2796, 40402, -39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig57 60013 14909 14957 1 48, 2805, 14909, -62 13 0 0 1 224 1 5747 ++ FBtr0300326 4823 2545 2844 contig56 55020 11121 16943 2 30,45, 2545,2799, 11121,16898, -39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig56 55020 44922 44970 1 48, 2805, 44922, -63 18 0 0 1 215 1 773 ++ FBtr0300326 4823 2539 2835 contig55 40015 6868 7722 2 33,48, 2539,2787, 6868,7674, -42 12 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2859 contig46 50012 18047 18101 1 54, 2805, 18047, -48 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2787 2844 contig41 60014 2335 2392 1 57, 2787, 2335, -57 21 0 0 0 0 0 0 ++ FBtr0300326 4823 2776 2854 contig41 60014 49022 49100 1 78, 2776, 49022, -69 15 0 0 1 224 1 25782 ++ FBtr0300326 4823 2538 2846 contig40 60015 6537 32403 2 36,48, 2538,2798, 6537,32355, -44 10 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig40 60015 51576 51630 1 54, 2799, 51576, -40 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig40 60015 24508 24556 1 48, 2805, 24508, -46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig38 50017 10792 10846 1 54, 2799, 10792, -39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2787 2835 contig38 50017 2022 2070 1 48, 2787, 2022, -46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig37 50013 25795 25849 1 54, 2799, 25795, -44 13 0 0 0 0 0 0 ++ FBtr0300326 4823 2789 2846 contig37 50013 6833 6890 1 57, 2789, 6833, -60 18 0 0 0 0 0 0 ++ FBtr0300326 4823 2775 2853 contig15 50014 30163 30241 1 78, 2775, 30163, -39 6 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig14 45010 5355 5400 1 45, 2798, 5355, -45 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig13 45015 20364 20418 1 54, 2799, 20364, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 32495 32543 1 48, 1838, 32495, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig32 40014 2484 2532 1 48, 1838, 2484, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig40 60015 54175 54223 1 48, 1838, 5792, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig41 60014 24166 24214 1 48, 1838, 35800, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig44 50013 36735 36783 1 48, 1838, 36735, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig45 50013 26731 26779 1 48, 1838, 26731, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig46 50012 1725 1773 1 48, 1838, 1725, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig46 50012 31347 31395 1 48, 1838, 18617, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 25367 25415 1 48, 1838, 25367, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 21863 21911 1 48, 1838, 21863, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 27528 27576 1 48, 1838, 27528, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 28391 28439 1 48, 1838, 28391, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 5360 5408 1 48, 1838, 5360, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 1858 1906 1 48, 1838, 1858, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 7523 7571 1 48, 1838, 7523, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 8386 8434 1 48, 1838, 8386, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig69 44962 39410 39458 1 48, 1838, 5504, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig70 55020 9457 9505 1 48, 1838, 45515, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig8 35012 30240 30288 1 48, 1838, 4724, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig9 60018 30240 30288 1 48, 1838, 29730, +42 6 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig30 70018 55429 55477 1 48, 1838, 55429, +42 6 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig31 40012 15422 15470 1 48, 1838, 15422, +42 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1889 contig31 40012 38731 38782 1 51, 1838, 38731, +42 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1889 contig32 40014 8720 8771 1 51, 1838, 8720, +43 5 0 0 0 0 1 32484 +- FBtr0070075 2430 1838 1886 contig65 45013 6838 39370 2 17,31, 1838,1855, 5643,38144, +58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig30 70018 41082 41916 2 48,21, 1838,2078, 41082,41895, +58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig31 40012 1075 1909 2 48,21, 1838,2078, 1075,1888, +54 15 0 0 0 0 0 0 +- FBtr0070120 4901 1857 1926 contig33 40016 5349 5418 1 69, 1857, 34598, 33 3 0 0 0 0 0 0 ++ FBtr0070135 2124 1891 1927 contig62 50017 15612 15648 1 36, 1891, 15612, 33 3 0 0 0 0 0 0 ++ FBtr0070136 2103 1870 1906 contig62 50017 15612 15648 1 36, 1870, 15612, 33 3 0 0 0 0 0 0 ++ FBtr0070137 2193 1960 1996 contig62 50017 15612 15648 1 36, 1960, 15612, +67 17 0 0 1 223 1 20545 +- FBtr0300326 4823 2538 2845 contig44 50013 3422 24051 2 36,48, 2538,2797, 25962,46543, +69 15 0 0 1 224 1 25782 ++ FBtr0300326 4823 2538 2846 contig40 60015 6537 32403 2 36,48, 2538,2798, 6537,32355, +72 18 0 0 1 231 1 292 ++ FBtr0300326 4823 2538 2859 contig58 50011 15076 15458 2 27,63, 2538,2796, 15076,15395, +76 14 0 0 1 224 1 159 +- FBtr0300326 4823 2538 2852 contig23 50012 33494 33743 2 36,54, 2538,2798, 16269,16464, +63 18 0 0 1 215 1 773 ++ FBtr0300326 4823 2539 2835 contig55 40015 6868 7722 2 33,48, 2539,2787, 6868,7674, +69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig63 55021 23094 43969 2 33,54, 2540,2775, 11052,31873, +69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig64 40016 8089 28964 2 33,54, 2540,2775, 11052,31873, +62 13 0 0 1 224 1 5747 ++ FBtr0300326 4823 2545 2844 contig56 55020 11121 16943 2 30,45, 2545,2799, 11121,16898, +60 18 0 0 0 0 0 0 ++ FBtr0300326 4823 2775 2853 contig15 50014 30163 30241 1 78, 2775, 30163, +57 21 0 0 0 0 0 0 ++ FBtr0300326 4823 2776 2854 contig41 60014 49022 49100 1 78, 2776, 49022, +53 16 0 0 0 0 0 0 +- FBtr0300326 4823 2783 2852 contig3 40006 18576 18645 1 69, 2783, 21361, +39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2787 2835 contig38 50017 2022 2070 1 48, 2787, 2022, +45 12 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2844 contig32 40014 27422 27479 1 57, 2787, 12535, +48 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2787 2844 contig41 60014 2335 2392 1 57, 2787, 2335, +51 15 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2853 contig51 50015 23765 23831 1 66, 2787, 26184, +44 13 0 0 0 0 0 0 ++ FBtr0300326 4823 2789 2846 contig37 50013 6833 6890 1 57, 2789, 6833, +50 13 0 0 0 0 0 0 ++ FBtr0300326 4823 2796 2859 contig57 60013 40402 40465 1 63, 2796, 40402, +38 7 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig60 50013 39781 39826 1 45, 2798, 39781, +39 6 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig14 45010 5355 5400 1 45, 2798, 5355, +39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig53 50013 36486 36531 1 45, 2798, 13482, +39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig54 35008 16481 16526 1 45, 2798, 18482, +41 10 0 0 0 0 0 0 +- FBtr0300326 4823 2799 2850 contig6 40015 32155 32206 1 51, 2799, 7809, +44 10 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig40 60015 51576 51630 1 54, 2799, 51576, +45 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig13 45015 20364 20418 1 54, 2799, 20364, +46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig37 50013 25795 25849 1 54, 2799, 25795, +46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig38 50017 10792 10846 1 54, 2799, 10792, +47 10 0 0 0 0 0 0 +- FBtr0300326 4823 2801 2858 contig3 40006 825 882 1 57, 2801, 39124, +39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig56 55020 44922 44970 1 48, 2805, 44922, +39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig57 60013 14909 14957 1 48, 2805, 14909, +40 8 0 0 0 0 0 0 +- FBtr0300326 4823 2805 2853 contig12 56019 24590 24638 1 48, 2805, 31381, +40 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig40 60015 24508 24556 1 48, 2805, 24508, +42 12 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2859 contig46 50012 18047 18101 1 54, 2805, 18047, 52 6 0 0 0 0 1 871 +- FBtr0301569 2929 107 165 contig62 50017 15637 16566 2 18,40, 107,125, 33451,34340, -72 12 0 0 2 544 2 69 +- FBtr0301569 2929 1691 2319 contig33 40016 5316 5469 3 21,27,36, 1691,1815,2283, 34547,34605,34664, 92 40 0 0 1 516 0 0 +- FBtr0301569 2929 1680 2328 contig32 40014 20291 20423 2 69,63, 1680,2265, 19591,19660, 72 12 0 0 2 544 2 69 +- FBtr0301569 2929 1691 2319 contig32 40014 20318 20471 3 21,27,36, 1691,1815,2283, 19543,19601,19660, -52 6 0 0 0 0 1 871 +- FBtr0343166 3140 318 376 contig62 50017 15637 16566 2 18,40, 318,336, 33451,34340, -72 12 0 0 2 544 2 69 +- FBtr0343166 3140 1902 2530 contig33 40016 5316 5469 3 21,27,36, 1902,2026,2494, 34547,34605,34664, -107 32 0 0 2 498 2 41 +- FBtr0343166 3140 1902 2539 contig32 40014 20291 20471 5 19,39,12,6,63, 1902,1921,2025,2037,2476, 19543,19600,19639,19654,19660, -76 29 0 0 1 534 0 0 +- FBtr0343166 3140 1891 2530 contig32 40014 20318 20423 2 69,36, 1891,2494, 19591,19660, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig9 60018 30240 30288 1 48, 1838, 29730, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig9 60018 37825 37873 1 48, 1838, 22145, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig8 35012 30240 30288 1 48, 1838, 4724, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig70 55020 9457 9505 1 48, 1838, 45515, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig70 55020 2053 2101 1 48, 1838, 52919, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig7 50017 13278 13326 1 48, 1838, 36691, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig69 44962 39410 39458 1 48, 1838, 5504, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig69 44962 32006 32054 1 48, 1838, 12908, -50 10 0 0 0 0 0 0 +- FBtr0070075 2430 1826 1886 contig67 44531 31857 31917 1 60, 1826, 12614, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig66 45011 6949 6997 1 48, 1838, 38014, -43 5 0 0 0 0 1 32484 +- FBtr0070075 2430 1838 1886 contig65 45013 6838 39370 2 17,31, 1838,1855, 5643,38144, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig64 40016 6225 6273 1 48, 1838, 33743, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig63 55021 21230 21278 1 48, 1838, 33743, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig62 50017 34978 35026 1 48, 1838, 14991, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 23025 23073 1 48, 1838, 16935, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 1713 1761 1 48, 1838, 38247, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 38030 38078 1 48, 1838, 11935, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 16718 16766 1 48, 1838, 33247, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig6 40015 23282 23330 1 48, 1838, 16685, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig59 40011 22281 22329 1 48, 1838, 17682, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig58 50011 32281 32329 1 48, 1838, 17682, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig55 40015 14474 14522 1 48, 1838, 25493, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig51 50015 4265 4310 1 45, 1838, 45705, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig50 40009 19266 19311 1 45, 1838, 20698, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig5 50018 2777 2825 1 48, 1838, 47193, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig46 50012 31347 31395 1 48, 1838, 18617, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig41 60014 24166 24214 1 48, 1838, 35800, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig40 60015 54175 54223 1 48, 1838, 5792, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig4 55011 27779 27827 1 48, 1838, 27184, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig36 45010 8000 8045 1 45, 1838, 36965, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig35 48011 33007 33052 1 45, 1838, 14959, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig33 40016 10953 11001 1 48, 1838, 29015, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig32 40014 25955 26003 1 48, 1838, 14011, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig31 40012 15807 15852 1 45, 1838, 24160, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig30 70018 55814 55859 1 45, 1838, 14159, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig3 40006 37781 37829 1 48, 1838, 2177, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig25 75023 42521 42569 1 48, 1838, 32454, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig25 75023 20928 20973 1 45, 1838, 54050, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig24 40010 29304 29349 1 45, 1838, 10661, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig23 50012 49307 49352 1 45, 1838, 660, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig2 45017 14607 14655 1 48, 1838, 30362, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig15 50014 19711 19759 1 48, 1838, 30255, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig14 45010 23718 23766 1 48, 1838, 21244, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig13 45015 38726 38774 1 48, 1838, 6241, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig11 35013 7985 8030 1 45, 1838, 26983, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig10 43013 28990 29035 1 45, 1838, 13978, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig1 45179 29774 29822 1 48, 1838, 15357, -69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig64 40016 8089 28964 2 33,54, 2540,2775, 11052,31873, -69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig63 55021 23094 43969 2 33,54, 2540,2775, 11052,31873, -41 10 0 0 0 0 0 0 +- FBtr0300326 4823 2799 2850 contig6 40015 32155 32206 1 51, 2799, 7809, -39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig54 35008 16481 16526 1 45, 2798, 18482, -39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig53 50013 36486 36531 1 45, 2798, 13482, -51 15 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2853 contig51 50015 23765 23831 1 66, 2787, 26184, -67 17 0 0 1 223 1 20545 +- FBtr0300326 4823 2538 2845 contig44 50013 3422 24051 2 36,48, 2538,2797, 25962,46543, -45 12 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2844 contig32 40014 27422 27479 1 57, 2787, 12535, -47 10 0 0 0 0 0 0 +- FBtr0300326 4823 2801 2858 contig3 40006 825 882 1 57, 2801, 39124, -53 16 0 0 0 0 0 0 +- FBtr0300326 4823 2783 2852 contig3 40006 18576 18645 1 69, 2783, 21361, -76 14 0 0 1 224 1 159 +- FBtr0300326 4823 2538 2852 contig23 50012 33494 33743 2 36,54, 2538,2798, 16269,16464, -40 8 0 0 0 0 0 0 +- FBtr0300326 4823 2805 2853 contig12 56019 24590 24638 1 48, 2805, 31381, -54 15 0 0 0 0 0 0 +- FBtr0070120 4901 1857 1926 contig33 40016 5349 5418 1 69, 1857, 34598, +72 12 0 0 2 544 2 69 +- FBtr0301569 2929 1691 2319 contig33 40016 5316 5469 3 21,27,36, 1691,1815,2283, 34547,34605,34664, +46 8 0 0 0 0 0 0 ++ FBtr0307554 3546 2975 3029 contig55 40015 26192 26246 1 54, 2975, 26192, +46 8 0 0 0 0 0 0 ++ FBtr0307555 4528 3113 3167 contig55 40015 26192 26246 1 54, 3113, 26192, 54 15 0 0 0 0 0 0 +- FBtr0340081 4889 1857 1926 contig33 40016 5349 5418 1 69, 1857, 34598, 54 15 0 0 0 0 0 0 +- FBtr0340082 4657 1613 1682 contig33 40016 5349 5418 1 69, 1613, 34598, +52 6 0 0 0 0 1 871 +- FBtr0343166 3140 318 376 contig62 50017 15637 16566 2 18,40, 318,336, 33451,34340, +76 29 0 0 1 534 0 0 +- FBtr0343166 3140 1891 2530 contig32 40014 20318 20423 2 69,36, 1891,2494, 19591,19660, +107 32 0 0 2 498 2 41 +- FBtr0343166 3140 1902 2539 contig32 40014 20291 20471 5 19,39,12,6,63, 1902,1921,2025,2037,2476, 19543,19600,19639,19654,19660, +72 12 0 0 2 544 2 69 +- FBtr0343166 3140 1902 2530 contig33 40016 5316 5469 3 21,27,36, 1902,2026,2494, 34547,34605,34664,
--- a/test-data/dbia3/dbia3_masked.sorted.psl Thu May 31 11:25:53 2018 -0400 +++ b/test-data/dbia3/dbia3_masked.sorted.psl Mon Jul 09 13:07:54 2018 -0400 @@ -1,61 +1,61 @@ -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig14 45010 22563 22611 1 48, 1838, 22563, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig65 45013 12112 12160 1 48, 1838, 12112, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig64 40016 32121 32169 1 48, 1838, 32121, +50 10 0 0 0 0 0 0 +- FBtr0070075 2430 1826 1886 contig67 44531 31857 31917 1 60, 1826, 12614, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig25 75023 20928 20973 1 45, 1838, 54050, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig50 40009 19266 19311 1 45, 1838, 20698, +38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig51 50015 4265 4310 1 45, 1838, 45705, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51622 51670 1 48, 1838, 51622, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1607 1655 1 48, 1838, 1607, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig32 40014 25955 26003 1 48, 1838, 14011, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig33 40016 10953 11001 1 48, 1838, 29015, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 16718 16766 1 48, 1838, 33247, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 1713 1761 1 48, 1838, 38247, 39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig63 55021 47126 47174 1 48, 1838, 47126, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 7523 7571 1 48, 1838, 7523, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 1858 1906 1 48, 1838, 1858, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 29934 29982 1 48, 1838, 29934, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 27528 27576 1 48, 1838, 27528, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 21863 21911 1 48, 1838, 21863, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 1146 1194 1 48, 1838, 1146, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig51 50015 31154 31202 1 48, 1838, 31154, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig50 40009 30606 30654 1 48, 1838, 30606, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig6 40015 23282 23330 1 48, 1838, 16685, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig64 40016 32121 32169 1 48, 1838, 32121, +39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig65 45013 12112 12160 1 48, 1838, 12112, +39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig7 50017 13278 13326 1 48, 1838, 36691, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig13 45015 37571 37619 1 48, 1838, 37571, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig14 45010 22563 22611 1 48, 1838, 22563, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51865 51913 1 48, 1838, 51865, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1850 1898 1 48, 1838, 1850, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig38 50017 35343 35391 1 48, 1838, 35343, 40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig39 45019 20340 20388 1 48, 1838, 20340, 40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig39 45019 7999 8047 1 48, 1838, 7999, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig38 50017 35343 35391 1 48, 1838, 35343, -58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig31 40012 1075 1909 2 48,21, 1838,2078, 1075,1888, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig50 40009 30606 30654 1 48, 1838, 30606, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig51 50015 31154 31202 1 48, 1838, 31154, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig52 40012 1146 1194 1 48, 1838, 1146, +40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 29934 29982 1 48, 1838, 29934, +40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig66 45011 6949 6997 1 48, 1838, 38014, +41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig15 50014 19711 19759 1 48, 1838, 30255, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 61212 61260 1 48, 1838, 61212, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 21863 21911 1 48, 1838, 21863, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig53 50013 27528 27576 1 48, 1838, 27528, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 1858 1906 1 48, 1838, 1858, +41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig54 35008 7523 7571 1 48, 1838, 7523, +43 5 0 0 0 0 1 32484 +- FBtr0070075 2430 1838 1886 contig65 45013 6838 39370 2 17,31, 1838,1855, 5643,38144, 58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig30 70018 41082 41916 2 48,21, 1838,2078, 41082,41895, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1850 1898 1 48, 1838, 1850, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig26 40013 1607 1655 1 48, 1838, 1607, -41 7 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 61212 61260 1 48, 1838, 61212, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51865 51913 1 48, 1838, 51865, -39 9 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig25 75023 51622 51670 1 48, 1838, 51622, -40 8 0 0 0 0 0 0 ++ FBtr0070075 2430 1838 1886 contig13 45015 37571 37619 1 48, 1838, 37571, -38 7 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig60 50013 39781 39826 1 45, 2798, 39781, +58 11 0 0 1 192 1 765 ++ FBtr0070075 2430 1838 2099 contig31 40012 1075 1909 2 48,21, 1838,2078, 1075,1888, +67 17 0 0 1 223 1 20545 +- FBtr0300326 4823 2538 2845 contig44 50013 3422 24051 2 36,48, 2538,2797, 25962,46543, +68 16 0 0 1 231 1 17935 ++ FBtr0300326 4823 2538 2853 contig40 60015 6537 24556 2 36,48, 2538,2805, 6537,24508, 68 16 0 0 1 231 1 292 ++ FBtr0300326 4823 2538 2853 contig58 50011 15076 15452 2 27,57, 2538,2796, 15076,15395, -46 11 0 0 0 0 0 0 ++ FBtr0300326 4823 2796 2853 contig57 60013 40402 40459 1 57, 2796, 40402, -39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig57 60013 14909 14957 1 48, 2805, 14909, -62 13 0 0 1 224 1 5747 ++ FBtr0300326 4823 2545 2844 contig56 55020 11121 16943 2 30,45, 2545,2799, 11121,16898, -39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig56 55020 44922 44970 1 48, 2805, 44922, +76 14 0 0 1 224 1 159 +- FBtr0300326 4823 2538 2852 contig23 50012 33494 33743 2 36,54, 2538,2798, 16269,16464, 63 18 0 0 1 215 1 773 ++ FBtr0300326 4823 2539 2835 contig55 40015 6868 7722 2 33,48, 2539,2787, 6868,7674, -42 12 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2859 contig46 50012 18047 18101 1 54, 2805, 18047, +69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig63 55021 23094 43969 2 33,54, 2540,2775, 11052,31873, +69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig64 40016 8089 28964 2 33,54, 2540,2775, 11052,31873, +62 13 0 0 1 224 1 5747 ++ FBtr0300326 4823 2545 2844 contig56 55020 11121 16943 2 30,45, 2545,2799, 11121,16898, 57 21 0 0 0 0 0 0 ++ FBtr0300326 4823 2776 2854 contig41 60014 49022 49100 1 78, 2776, 49022, -68 16 0 0 1 231 1 17935 ++ FBtr0300326 4823 2538 2853 contig40 60015 6537 24556 2 36,48, 2538,2805, 6537,24508, -46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig38 50017 10792 10846 1 54, 2799, 10792, -46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig37 50013 25795 25849 1 54, 2799, 25795, +45 12 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2844 contig32 40014 27422 27479 1 57, 2787, 12535, +51 15 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2853 contig51 50015 23765 23831 1 66, 2787, 26184, +46 11 0 0 0 0 0 0 ++ FBtr0300326 4823 2796 2853 contig57 60013 40402 40459 1 57, 2796, 40402, +38 7 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig60 50013 39781 39826 1 45, 2798, 39781, 39 6 0 0 0 0 0 0 ++ FBtr0300326 4823 2798 2843 contig14 45010 5355 5400 1 45, 2798, 5355, +39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig53 50013 36486 36531 1 45, 2798, 13482, +39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig54 35008 16481 16526 1 45, 2798, 18482, +41 10 0 0 0 0 0 0 +- FBtr0300326 4823 2799 2850 contig6 40015 32155 32206 1 51, 2799, 7809, 45 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig13 45015 20364 20418 1 54, 2799, 20364, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig7 50017 13278 13326 1 48, 1838, 36691, -50 10 0 0 0 0 0 0 +- FBtr0070075 2430 1826 1886 contig67 44531 31857 31917 1 60, 1826, 12614, -40 8 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig66 45011 6949 6997 1 48, 1838, 38014, -43 5 0 0 0 0 1 32484 +- FBtr0070075 2430 1838 1886 contig65 45013 6838 39370 2 17,31, 1838,1855, 5643,38144, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig61 40008 1713 1761 1 48, 1838, 38247, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig60 50013 16718 16766 1 48, 1838, 33247, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig6 40015 23282 23330 1 48, 1838, 16685, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig51 50015 4265 4310 1 45, 1838, 45705, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig50 40009 19266 19311 1 45, 1838, 20698, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig33 40016 10953 11001 1 48, 1838, 29015, -39 9 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig32 40014 25955 26003 1 48, 1838, 14011, -38 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1883 contig25 75023 20928 20973 1 45, 1838, 54050, -41 7 0 0 0 0 0 0 +- FBtr0070075 2430 1838 1886 contig15 50014 19711 19759 1 48, 1838, 30255, -69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig64 40016 8089 28964 2 33,54, 2540,2775, 11052,31873, -69 18 0 0 1 202 1 20788 +- FBtr0300326 4823 2540 2829 contig63 55021 23094 43969 2 33,54, 2540,2775, 11052,31873, -41 10 0 0 0 0 0 0 +- FBtr0300326 4823 2799 2850 contig6 40015 32155 32206 1 51, 2799, 7809, -39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig54 35008 16481 16526 1 45, 2798, 18482, -39 6 0 0 0 0 0 0 +- FBtr0300326 4823 2798 2843 contig53 50013 36486 36531 1 45, 2798, 13482, -51 15 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2853 contig51 50015 23765 23831 1 66, 2787, 26184, -67 17 0 0 1 223 1 20545 +- FBtr0300326 4823 2538 2845 contig44 50013 3422 24051 2 36,48, 2538,2797, 25962,46543, -45 12 0 0 0 0 0 0 +- FBtr0300326 4823 2787 2844 contig32 40014 27422 27479 1 57, 2787, 12535, +46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig37 50013 25795 25849 1 54, 2799, 25795, +46 8 0 0 0 0 0 0 ++ FBtr0300326 4823 2799 2853 contig38 50017 10792 10846 1 54, 2799, 10792, 47 10 0 0 0 0 0 0 +- FBtr0300326 4823 2801 2858 contig3 40006 825 882 1 57, 2801, 39124, -76 14 0 0 1 224 1 159 +- FBtr0300326 4823 2538 2852 contig23 50012 33494 33743 2 36,54, 2538,2798, 16269,16464, +39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig56 55020 44922 44970 1 48, 2805, 44922, +39 9 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2853 contig57 60013 14909 14957 1 48, 2805, 14909, 40 8 0 0 0 0 0 0 +- FBtr0300326 4823 2805 2853 contig12 56019 24590 24638 1 48, 2805, 31381, +42 12 0 0 0 0 0 0 ++ FBtr0300326 4823 2805 2859 contig46 50012 18047 18101 1 54, 2805, 18047,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 09 13:07:54 2018 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- required tools: + - blat + - sort + - pslReps + - faPolyASizes + - pslCDnaFilter + --> + <package name="ucsc_tools_340_for_BLAT" version="1.0"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme> + </package> +</tool_dependency> \ No newline at end of file