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changeset 0:7c2e9bc2123b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
author iuc
date Wed, 05 May 2021 15:09:54 +0000
parents
children 02831bf9e95f
files pretext_map.xml test-data/fullmap1.jpg test-data/fullmap2.bmp test-data/map.pretext test-data/output_1.pretext test-data/output_2.pretext test-data/output_3.pretext test-data/snapshot1.jpg test-data/snapshot2.jpg test-data/snapshot3.jpg test-data/test.bam test-data/test.sam
diffstat 12 files changed, 232 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pretext_map.xml	Wed May 05 15:09:54 2021 +0000
@@ -0,0 +1,132 @@
+<tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.5</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
+        <requirement type="package" version="1.12">samtools</requirement>
+    </requirements>
+    <version_command>PretextMap --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input.is_of_type("bam"):
+            samtools view -h '${input}' |
+        #else
+            cat '${input}' |
+        #end if
+        PretextMap
+        #if $sorting.sortby == "length":
+            --sortby length
+            --sortorder $sorting.sortorder
+        #elif $sorting.sortby == "name":
+            --sortby name
+            --sortorder $sorting.sortorder
+        #end if
+        #if $map_qual:
+            --mapq $map_qual
+        #end if
+        #if $filter.filter_type == "in":
+            --filterInclude '$filter.filter_list'
+        #elif $filter.filter_type == "out":
+            --filterExclude '$filter.filter_list'
+        #end if 
+        -o output.pretext
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
+        <conditional name="sorting">
+            <param argument="--sortby" type="select" label="Sort by">
+                <option value="nosort" selected="true">Don't sort</option>
+                <option value="length">Length</option>
+                <option value="name">Name</option>
+            </param>
+            <when value="nosort"/>
+            <when value="length">
+                <param argument="--sortorder" type="select" label="Sort order: ">
+                    <option value="ascend">Ascending</option>
+                    <option value="decend">Decending</option>
+                </param>
+            </when>
+            <when value="name">
+                <param argument="--sortorder" type="select" label="Sort order: ">
+                    <option value="ascend">Ascending</option>
+                    <option value="descend">Decending</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/>
+        <conditional name="filter">
+            <param name="filter_type" type="select" label="How to filter: ">
+                <option value="" selected="true">No filter</option>
+                <option value="in">Filter to include only specified sequence names</option>
+                <option value="out">Filter to exclude specified sequence names</option>
+            </param>
+            <when value=""/>
+            <when value="in">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                    <sanitizer>
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="out">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                    <sanitizer>
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="bam" value="test.bam"/>
+            <conditional name="sorting">
+                <param name="sortby" value="length"/>
+                <param name="sortorder" value="ascend"/>
+            </conditional>
+            <conditional name="filter">
+                <param name="filter_type" value="in"/>
+                <param name="filter_list" value="ref"/>
+            </conditional>
+            <param name="map_qual" value="10"/>
+            <output name="pretext_map_out" file="output_1.pretext"/>
+        </test>
+        <test>
+            <param name="input" ftype="sam" value="test.sam"/>
+            <conditional name="sorting">
+                <param name="sortby" value="name"/>
+                <param name="sortorder" value="descend"/>
+            </conditional>
+            <conditional name="filter">
+                <param name="filter_type" value="out"/>
+                <param name="filter_list" value="chrM, chr8, chr9"/>
+            </conditional>
+            <output name="pretext_map_out" file="output_2.pretext"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What is does**
+
+The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps.
+Pretext has no special requirement on the alignment files
+process your alignments however you want before feeding to PretextMap.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{Harry_et_al,
+            Author={Harry, E},
+            title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
+            url = {https://github.com/wtsi-hpag/PretextSnapshot},}
+        </citation>
+    </citations>
+</tool>
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Binary file test-data/output_1.pretext has changed
Binary file test-data/output_2.pretext has changed
Binary file test-data/output_3.pretext has changed
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Binary file test-data/snapshot3.jpg has changed
Binary file test-data/test.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.sam	Wed May 05 15:09:54 2021 +0000
@@ -0,0 +1,100 @@
+HWI-EAS269B:8:34:797:623	145	chr1	16632182	255	27M	=	16631977	0	CCATTTCCTGTATGCTGTAAAGTACAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:40:39:1184	145	chr1	24620331	3	27M	=	24620115	0	ATTTATGTGGTTTCGTTTACCTTCTAT	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:chrM	CP:i:9060
+HWI-EAS269B:8:58:533:1198	81	chr1	88426079	255	27M	=	88423429	0	GAAGAGGAAGAAGGTGGGGAGGAAGAG	IIIG?IIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:89:1776:1815	97	chr1	134085638	255	27M	=	134085824	0	GAATGATTCTCTGGGTGTTACTTTGCA	IIIIIIIIIIIIIIIDIII:IIII>F5	NM:i:0	NH:i:1
+HWI-EAS269B:8:74:1134:1670	161	chr1	138166886	255	27M	=	138167084	0	TTACTAGTGTCTCTCTTACCATCATAT	.IIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:1
+HWI-EAS269:3:59:1321:1427	147	chr1	173149715	255	27M	=	173149555	0	AAGGGCTAGGGTGACAGGCAGGGGACG	-C<CID?IIIIIIIDIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:8:164:1678	145	chr1	178660716	255	27M	=	178660493	0	CAATTGGTGTTTTTCTTAAGAGACTCA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:1:1048:638	137	chr10	12456478	1	27M	*	0	0	TAAAANAAATAAAACAAAACAATAAAA	$'&(+")'%$(&*&#&$$#%%$$%%$$	NM:i:2	NH:i:4	CC:Z:chr16	CP:i:21639623
+HWI-EAS269:3:62:1211:798	147	chr10	28135294	255	27M	=	28135117	0	ACATGGTGTGGGGACAGAGATGTGAAG	I;IIIIIIAIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:1
+HWI-EAS269:3:27:410:424	145	chr10	76950070	255	27M	=	76949871	0	GAGTCTGTGTCCAGGCCAATTCACTAT	25-8I+.6B.IIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:48:1180:1122	73	chr10	83772157	0	27M	*	0	0	GATCATCTTTTCTAAAACAATAAAGAC	/IIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:6	CC:Z:chr11	CP:i:93811140
+HWI-EAS269:3:77:654:131	99	chr10	93419810	255	27M	=	93419993	0	TTGCATCCCTAGGAACTGGAGTTATAG	IIIIIIGIHIIIED@CIIH5I3D9G6:	NM:i:0	NH:i:1
+HWI-EAS269B:8:98:895:1810	177	chr11	3371472	255	27M	=	37952212	0	CTACATAGTGGGAACCGGCGACCGCTG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:2	NH:i:1
+HWI-EAS269B:8:58:1126:883	97	chr11	30080486	255	27M	=	30080702	0	TACTTCCACCAGGCTCCAGTTTTGTGA	IIIIIIIIIIIIIIIIIIIIIIIIII5	NM:i:0	NH:i:1
+HWI-EAS269B:8:89:1763:1446	81	chr11	59589605	255	27M	=	59589400	0	GTACCTGGCCACTGATGCAGCTTAGAA	II<IIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:6:739:1329	161	chr11	68629628	3	27M	=	68629835	0	GTTTTTGGTTGATAGTTGAGCAAACTG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:chr4	CP:i:126661877
+HWI-EAS269:3:19:1683:1350	81	chr11	70846915	255	27M	=	70846725	0	CACGGGCAGATAAGCTGCTGAGACTAA	H50BB:IF=IIGIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:9:1691:1087	97	chr11	84640783	255	27M	=	84641010	0	ACATTATCCATCTCTCTGTCATTGTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:48:1350:424	81	chr11	94150331	255	27M	=	94150113	0	TTGCAAGCCAACCCTGAGTGAAGTGTC	IIDHIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:22:1176:1405	97	chr11	98629843	255	27M	=	98630030	0	CCCTCGGAGGGCAACGGGAAAGGAGAA	IIIIIIIIIIIDIIIII?III/79E14	NM:i:0	NH:i:1
+HWI-EAS269:3:67:1311:1512	97	chr11	100488190	255	27M	=	100488374	0	CATGCCCTGAGACTTAGCAAGACTCTT	IIIIIIIIIIIIIIIEIA3,I57GBI@	NM:i:0	NH:i:1
+HWI-EAS269B:8:41:1142:1307	161	chr11	101320424	255	27M	=	101320625	0	GCCTCCCTACATAGCAAAGGAAAGAAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:31:1101:21	97	chr11	116711287	255	27M	=	116711485	0	CATAAGCAAAAGATACACCATGTTTTA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:84:637:1203	145	chr12	35829424	255	27M	=	35829229	0	CTCCCTCAAGGATCTTGTGGGGCATCA	</'>I,I5B26$II;EB=%IIII1III	NM:i:0	NH:i:1
+HWI-EAS269:3:65:1158:1081	163	chr12	52234332	255	27M	=	52234505	0	TTTTTTTTTTAAGACAGGGAGTTTTTT	IIIIIIIIIIIC4,,*>II%-,%III>	NM:i:1	NH:i:1
+HWI-EAS269B:8:65:1325:1287	137	chr12	52234513	3	27M	*	0	0	GCAGCACCTTGTGACATTTAATTTAGT	IIIII+IIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:chr15	CP:i:98780443
+HWI-EAS269:3:38:488:1093	97	chr12	80471642	255	27M	=	80471839	0	TGGAGAGATGACTCCTTGTTTGAGACA	IIIIIIIIIIIIIIIIIIIBAE0B<7D	NM:i:0	NH:i:1
+HWI-EAS269:3:76:290:1451	99	chr12	117745566	0	27M	=	117745739	0	CAATCTGAAGATCCACAATCTTTTATA	IIIIIIIIIIIIIIFII5I9IIII+I7	NM:i:0	NH:i:5	CC:Z:chr4	CP:i:133520935
+HWI-EAS269B:8:39:353:1526	65	chr13	18122558	255	27M	=	18122761	0	ACTCTACTCAAAACCACACTAAGCCTC	@IIIIII6IIIIIDII9IIIIII<III	NM:i:0	NH:i:1
+HWI-EAS269:3:63:1260:365	99	chr13	41278147	255	27M	=	41278319	0	AAGACAAGAACTTATCCACCAATATGT	IIIIIIIIIIIIIII<IIA<CIIDII>	NM:i:0	NH:i:1
+HWI-EAS269:3:70:152:1609	161	chr13	55421426	255	27M	=	55421687	0	CGCTTGACCATTCCAGCCCAGACAAGA	IIIIIIIII8IIII3IIII-C(3-%B'	NM:i:0	NH:i:1
+HWI-EAS269:3:9:1343:1414	99	chr13	83721797	255	27M	=	83721967	0	AACTACAGCTGAGGCAGCCTCCTGCCT	IIIIIIIIIIIIIIIII;E+?7&819&	NM:i:0	NH:i:1
+HWI-EAS269:3:4:1480:1956	137	chr14	46703849	0	27M	*	0	0	GTGGAGCCCAGTGACACCATCGAGAAC	IIIIIIIIIIIII?C3IH?1@I@@=27	NM:i:0	NH:i:8	CC:Z:=	CP:i:46704077
+HWI-EAS269:3:86:616:1519	137	chr14	56244763	255	27M	*	0	0	CATGGCCTGAAGTTCCTGAGCTTTATC	IIIIIIIII3DIBI9II3)73BIG'G+	NM:i:0	NH:i:1
+HWI-EAS269:3:42:656:1216	97	chr14	100271567	255	27M	=	100271751	0	ATAAGTCTCAGTTCTTGGGCCAGATCA	IIIIIIIIICIIIIII3IA854I1C+)	NM:i:0	NH:i:1
+HWI-EAS269:3:87:95:767	73	chr16	7368880	255	27M	*	0	0	AATATCTGAAACATTCAAATGAGCAAT	F>II/4I@9H=II?IIIIIIIIIIII-	NM:i:0	NH:i:1
+HWI-EAS269B:8:50:1572:711	145	chr16	32230400	255	27M	=	32230196	0	TACAGCAACAACAAATTCAACGACACG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:56:1436:121	147	chr16	49887529	255	27M	=	49887356	0	TTAAGGCCCAGCTCTACATAAAACACT	IIIIAHIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:53:584:1696	99	chr17	45705815	255	27M	=	45705987	0	CCTTCTTGTCCAAGATCTCCTTCATGA	IIIIIIIIIIIIBI6IIII=II:GI@<	NM:i:0	NH:i:1
+HWI-EAS269B:8:16:643:1950	177	chr18	38000738	255	27M	=	38000570	0	ATTCTGGTTCAGCCTGGGCAGCTTGGG	III@==I0<IIGIII;IIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:66:1760:1539	137	chr18	38624681	3	27M	*	0	0	TTTGGAACTTTTGAGAGGATCCCTAGC	IIIIIIIIIIIIIII1II.IIIII1II	NM:i:0	NH:i:2
+HWI-EAS269:3:2:1723:1277	163	chr19	16341705	255	27M	=	16341870	0	ATGGGCTCGTCGCAGCTCAGCGGCTGG	IIIIIIIIIIIIICI=8<&I7:F(+;2	NM:i:1	NH:i:1
+HWI-EAS269B:8:66:317:1676	97	chr19	47099316	255	27M	=	47099535	0	ATCTGGTCAATCAACACCACCAGCAGA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:10:1428:1315	81	chr2	22444224	3	27M	=	22444039	0	GGAATTGCGATAATTATAGTGGCTGAT	?6>CI>GIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:chrM	CP:i:6245
+HWI-EAS269:3:72:152:785	97	chr2	22796881	255	27M	=	22797074	0	TGAGTACTCCAGATAATCGTTACACAA	IIIIIIII6IIIIIIII0IA@?,7752	NM:i:0	NH:i:1
+HWI-EAS269:3:79:321:1095	99	chr2	62083760	255	27M	=	62083938	0	CAAAAATTGAGATATCAAAAAGCTCTT	IIIIIIIII2IGIBIIC8:4IB1H4I;	NM:i:0	NH:i:1
+HWI-EAS269:3:93:1529:881	97	chr2	129998362	255	27M	=	129998827	0	CGCATGCCAGGAGGGGGCATGCCCATT	IIIFIIIIFIIIIIFII?72I.,020*	NM:i:0	NH:i:1
+HWI-EAS269B:8:20:813:376	113	chr2	130534278	255	27M	=	130534454	0	TGTATTAGCAGGAGGTGGGGAGGCTGA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:89:1221:1082	83	chr2	151285071	0	27M	=	151284944	0	ACCAGTGCACAGGTCTCCAGGGCTTCT	-IC=B+8IIIEIIFI5IIIIIIIIIII	NM:i:0	NH:i:5	CC:Z:chr9	CP:i:31743980
+HWI-EAS269:3:66:46:336	163	chr2	156679837	255	27M	=	156680016	0	TATTTTCCTTTTGCTGTGGTTTGTGTT	IIIIIIIIIIIIIEI@E-I?GI&B%3I	NM:i:0	NH:i:1
+HWI-EAS269B:8:52:1139:1381	73	chr2	174953004	0	27M	*	0	0	AATGCTCAACTCTTAGTTTCTTATTCA	IIIIIIIIIIIIIIIIB@?IIIII?+0	NM:i:0	NH:i:19	CC:Z:=	CP:i:175018018
+HWI-EAS269:3:98:585:19	161	chr3	26005087	255	27M	=	26005271	0	ACCTAACACATGTAAACTTAAATTCAT	I:IIIIIIII<IIE==DDI):,D1--8	NM:i:0	NH:i:1
+HWI-EAS269:3:74:447:1309	83	chr3	80492396	255	27M	=	80492220	0	TCGGATGCCTCTCACCACTTTGACAAT	)H():F=85IIIIEIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:74:425:1427	161	chr3	96447603	255	27M	=	96447820	0	TGGAGTAGGAGTCTCAGGAGGAGTAGA	IIIIIIIIIIIIIIIIIIIII:I?II<	NM:i:0	NH:i:1
+HWI-EAS269:3:10:739:1474	163	chr3	124089371	255	27M	=	124089535	0	AAAAAAACAATCTTATTCCGAGCATTC	IIIIIIIIIIIIIIIIIIIIIIIGIII	NM:i:0	NH:i:1
+HWI-EAS269:3:20:357:1709	65	chr4	128895987	255	27M	=	128895822	0	CCTACCTTCTTCCCTTGGCAGCTGACT	IIII>IIIBIIA:I18):,*3&,/*'+	NM:i:0	NH:i:1
+HWI-EAS269B:8:22:623:129	113	chr4	135492867	255	27M	=	135490613	0	CCACTTTCCTGTACTGGCCAGAAAATG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:48:824:702	65	chr4	139584010	255	27M	=	139582899	0	CTGGGCAGTGCAGCGGTACATGGAGCC	IIIIIIIIIIIIIIIIII<AIIB;I>:	NM:i:0	NH:i:1
+HWI-EAS269B:8:33:527:1211	73	chr5	37627410	255	27M	*	0	0	GGGAAGGTGTGAGTACAACAGCCAAAG	IIIIIIIIIIIIIIIIIIIIIIII@II	NM:i:0	NH:i:1
+HWI-EAS269:3:2:1518:599	163	chr5	136908928	255	27M	=	136909101	0	CTATTGCCAAAAAACTATGTTCACAAA	IIIIIIIIIIIIIIIIIIIIIIIII=I	NM:i:0	NH:i:1
+HWI-EAS269B:8:62:1493:1455	161	chr5	138715332	255	27M	=	138715534	0	CCCAAATGAAAAAATAAATATTATGAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:69:384:1894	147	chr5	143665243	255	27M	=	143665064	0	TGTTTGCTCCAACCAACTGCTGTCGCC	&++*,2H-IGI+IFIGI?IIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:56:1358:762	113	chr6	15024174	255	7M12235N20M	=	51485453	0	TGGGTACTTTCTCTAGCTCCTCCATTG	/@)3I?IIIIIIIIIIIIIIIIIIIII	NM:i:2	XS:A:-	NH:i:1
+HWI-EAS269:3:100:228:1799	163	chr6	37756378	3	27M	=	37756558	0	GTGTGGGGCTGCGTGGCCTGGCTGGTG	DII4A+>5EI.)F634820&1(0%&&&	NM:i:2	NH:i:2
+HWI-EAS269B:8:50:188:1253	161	chr6	52296684	1	27M	=	52296901	0	ACTTTTCAGGGTTTTCAATAGTCACAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:3	CC:Z:=	CP:i:140695441
+HWI-EAS269B:8:19:440:1687	161	chr6	52850377	255	27M	=	52850580	0	TACAAAGATGGACTTTTAAAATTCATT	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:47:1555:1520	161	chr6	67231655	255	27M	=	67233919	0	ATTCAGTTATGGACCATCATTTCCGGA	IIIIIIIIIIIIIIIIIIIIII<AII1	NM:i:0	NH:i:1
+HWI-EAS269B:8:79:1563:1318	161	chr6	89267414	255	27M	=	89267614	0	GTGCGTGTTCCAGGCAGAGCTGGAAGA	IIIIIIIIIIIIIIIIIIIIIII=;IA	NM:i:0	NH:i:1
+HWI-EAS269B:8:54:954:565	161	chr6	120882513	255	27M	=	120882716	0	ACGTCATGGCTGACCAGGACAGAGGTG	IIIIIIIIIIIIIII?IEG;II<II*8	NM:i:0	NH:i:1
+HWI-EAS269B:8:16:570:1775	145	chr7	26081268	255	27M	=	26080313	0	GAAAGAGTGACACAAATCAATAGTAAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:13:280:189	161	chr7	29184615	255	27M	=	29184814	0	CTTTTCCAACAGCGAGAAAAATGTACA	IIIIIIIIIIIIIIIIIIIIIIIIDII	NM:i:0	NH:i:1
+HWI-EAS269B:8:19:72:273	137	chr7	52258521	255	27M	*	0	0	ATCAGAGGCACAGGGACAGGGTAAGGA	&&2IIIII;E(IIIIIIIIIIIIIIII	NM:i:1	NH:i:1
+HWI-EAS269B:8:40:235:869	161	chr7	52631974	255	27M	=	52632179	0	GGCGCTGACTCCATCAGATATCCATTC	IIIIIII7IIIIIII6IIIIIIIBIII	NM:i:1	NH:i:1
+HWI-EAS269B:8:18:304:346	129	chr7	107789557	255	27M	=	33158390	0	CACGTACTGTCACCTTGTAACATTTGG	IIIIIIIIIIIIIIIIIIIIIIIIIIF	NM:i:0	NH:i:1
+HWI-EAS269B:8:3:698:297	161	chr7	110976065	255	27M	=	110976385	0	GCAGTTATCACTTTCTTGCCATGGGCC	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:50:1269:965	145	chr7	118217605	255	27M	=	118216239	0	ACCTGTAGATCCACATGATCATGAAGA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:38:1381:1429	83	chr7	136141344	255	27M	=	136141280	0	ATCTGAAGTATCCCACATGTTGAGCTC	<III@IIIIIIIII>IIIIIIIIIIII	NM:i:1	NH:i:1
+HWI-EAS269:3:25:781:386	83	chr8	29844005	255	27M	=	29843841	0	TAAGGGAGGAAAGTGTTTCAGAGTGTA	;83<159<<III@IIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:25:979:679	163	chr8	72664237	255	27M	=	72664413	0	CTGATGGGAGCCCTGCGTGGTAAGAGG	IIIIIIIIIII=III@I(II$27I>I4	NM:i:0	NH:i:1
+HWI-EAS269B:8:23:1069:816	145	chr8	74704433	255	27M	=	74704222	0	TGTTCTCAGTTGTGGACAAGTGACAGC	I<GII@IIIIIIII;IIIIIIIIII0I	NM:i:0	NH:i:1
+HWI-EAS269B:8:34:435:1679	73	chr8	87366211	3	27M	*	0	0	AAGCCTAGGGCTTCTCCTCTACACCCC	I556I;FCAIIIFI<IIIIIIIIIIII	NM:i:0	NH:i:2
+HWI-EAS269B:8:32:1486:294	97	chr8	124121215	255	27M	=	124121411	0	TGTTACCATACGCCCTTCTGCTGAGGC	IIIIIIIIIIIIIIIIIIDIIIIGIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:32:142:1471	81	chr8	124496752	3	27M	=	124496536	0	GGATCTGCTTCATGAGTTGCCACATTG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	NH:i:2
+HWI-EAS269B:8:60:82:1806	97	chr8	125945215	255	27M	=	125945423	0	AGATGCTGGCCATCCAGAGTAAGAACA	IIIIIIIIIIIIIIIIIIIHIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:16:1162:495	81	chr8	125945584	255	27M	=	125945381	0	GTTGCTCGCAGCTGGGGTGTGGGGCCA	<CIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:1:165:1889	81	chr8	126016885	255	27M	=	126016469	0	TGAGCAGGAAAACACTTTAAACCAGAT	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:66:939:1154	145	chr9	17537149	255	27M	=	17536959	0	CTCCTTCAAGTACGCCTGGGTCTTAGA	IDIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:68:1189:285	81	chr9	61249807	255	27M	=	61242460	0	AGTCAAGCTCACTTGGCGGTGAAGGAT	@.0;;A,?-F5I;7IIIIGIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:15:784:1754	163	chr9	74846937	255	27M	=	74847108	0	GCACAGCACTGAGGAAAGGATCATCTC	IIIIIIIIIIIIIIIIIIGII1CI7II	NM:i:0	NH:i:1
+HWI-EAS269B:8:26:126:1382	145	chrM	3413	255	27M	=	3190	0	GTTATTCTTTATAGCAGAGTACACTAA	IIII8IB328I9IIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269:3:90:320:1336	73	chrM	6326	255	27M	*	0	0	ATGATCTCCAGCTATCCTATGAGCCTT	IIIIIIIIA.ICI.4'(=,C>7-*&@8	NM:i:1	NH:i:1
+HWI-EAS269B:8:23:469:1215	161	chrM	7472	3	27M	=	7676	0	ATTTCATCTGAAGACGTCCTCCACTCA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2
+HWI-EAS269:3:73:36:783	161	chrM	7958	3	27M	=	8152	0	CCCCAACAATAATAGGATTCCCAATCG	IIIIIIIIIIIIIIIIIIIII09I>>I	NM:i:0	NH:i:2
+HWI-EAS269:3:33:1528:954	99	chrM	8012	3	27M	=	8186	0	TCCTATTCCCATCCTCAAAACGCCTAA	IIIIIIIIIIIIIIIIIIIIIIIDII:	NM:i:0	NH:i:2
+HWI-EAS269:3:2:192:1456	161	chrM	9071	3	27M	=	9255	0	ACGAAACCACATAAATCAAGCCCTACT	III;IEIIDI7III+III*?I@CH+5I	NM:i:0	NH:i:2
+HWI-EAS269:3:63:192:470	97	chrM	14787	255	27M	=	14982	0	GCAGATAAAATTCCATTTCACCCCTAC	IIIIIIIIIIIIIIFIII=B5042:4E	NM:i:0	NH:i:1
+HWI-EAS269B:8:49:528:63	83	chrM	14963	255	27M	=	14829	0	TTTCCTATTTGCATACGCCATTCTACG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:98:856:1516	145	chrX	20257960	255	27M	=	20256746	0	TACCCGGATTTAAGATGTACCCCATTG	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:28:1174:110	145	chrX	53916348	255	27M	=	53916153	0	TGAATGTCAGCATCATTGACCCACAAA	IIIIFIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
+HWI-EAS269B:8:58:663:410	147	chrX	75006902	255	27M	=	75006834	0	TCAGGTGGTTTACAGTGTTCTGACAAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
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