changeset 1:7cd07dd27927 draft default tip

planemo upload for repository https://github.com/Yating-L/psltobigpsl.git commit 517f74861bea50f74aa36e15cf3239bbcd353e4f-dirty

--- a/psltobigpsl.xml	Fri Jan 20 17:00:09 2017 -0500
+++ b/psltobigpsl.xml	Wed Apr 12 17:38:51 2017 -0400
@@ -1,23 +1,90 @@
 <tool id="pslToBigPsl" name="pslToBigPsl" version="0.1.0">
     <requirements>
-        <!-- Requires Conda -->
-        <requirement type="package" version="0.1.0">psltoBigPsl</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        $__tool_directory__/pslToBigPsl $input stdout | sort -k1,1 -k2,2n > $output
+        $__tool_directory__/pslToBigPsl 
+            '${input}'
+            #if $add_input.input_type == "both"
+                -cds='${input_cds}'
+                -fa='${input_fa}'
+            #elif $add_input.input_type == "fa"
+                -fa='${input_fa}'
+            #elif $add_input.input_type == "cds"
+                -cds='${input_cds}'
+            #end if   
+            output
+            && sort -k1,1 -k2,2n output > '${output_sorted}'
     ]]></command>
     <inputs>
         <param name="input" label="Psl file" type="data" format="psl" />
+        <conditional name="add_input">
+            <param name="input_type" type="select" label="Provide FASTA and CDS files">
+                <option value="no">No</option>
+                <option value="both">Provide both FASTA and CDS files</option>
+                <option value="fa">Provide FASTA file</option>
+                <option value="cds">Provide CDS file</option>
+            </param>
+            <when value="both">
+                <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
+                <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
+            </when>
+             <when value="fa">
+                <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
+            </when>
+            <when value="cds">
+                <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="output" format="bed" />
+        <data name="output_sorted" format="bed" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="amaVit1_Gallus_gallus.psl" />
+            <param name="input_type" value="no" />
+            <output name="output_sorted" value="out.bigpsl" />
+        </test>
+        <test>
+            <param name="input" value="amaVit1_Gallus_gallus.psl" />
+            <param name="input_type" value="fa" />
+            <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
+            <output name="output_sorted" value="out_fa.bigpsl" />
+        </test>
+        <test>
+            <param name="input" value="amaVit1_Gallus_gallus.psl" />
+            <param name="input_type" value="cds" />
+            <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
+            <output name="output_sorted" value="out_cds.bigpsl" />
+        </test>
+        <test>
+            <param name="input" value="amaVit1_Gallus_gallus.psl" />
+            <param name="input_type" value="both" />
+            <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
+            <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
+            <output name="output_sorted" value="out_both.bigpsl" />
+        </test>
+    </tests>
     <help><![CDATA[
         Transform a Psl format file to a Bed format file.
         Input: Psl File
         Ouput: BigPsl File
     ]]></help>
+    <citations>
+            <citation type="bibtex">@article{kent2002blat,
+                  title={BLAT—the BLAST-like alignment tool},
+                  author={Kent, W James},
+                  journal={Genome research},
+                  volume={12},
+                  number={4},
+                  pages={656--664},
+                  year={2002},
+                  publisher={Cold Spring Harbor Lab}
+            }</citation>
+      </citations> 
 </tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gallus_gallus_RefSeq.cds	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,100 @@
+NM_001199713	95..1546
+NM_001199712	95..1618
+NM_001030697	100..2745
+NM_001277797	1..2943
+NM_001184757	1..468
+NM_205038	272..1336
+NM_204727	406..966
+NM_001031150	220..2043
+NM_204996	56..3379
+NM_001005808	216..1316
+NM_205405	26..4981
+NM_205387	19..312
+NM_001115017	48..2060
+NM_204843	170..1840
+NM_001347710	32..1513
+NM_001328355	99..1328
+NM_001328354	87..530
+NM_001278102	156..524
+NM_001278100	320..688
+NM_001278104	91..459
+NM_001006176	347..3118
+NM_001281486	21..248
+NM_001278545	42..728
+NM_001277657	250..774
+NM_001277490	21..818
+NM_001277477	81..569
+NM_001277476	81..569
+NM_001199231	141..365
+NM_001031013	121..822
+NM_001195562	1..2664
+NM_001194996	58..1314
+NM_001006577	58..1293
+NM_001145430	217..420
+NM_001110060	1..714
+NM_001044640	16..642
+NM_001030706	43..1413
+NM_001030974	38..1090
+NM_001031172	33..2396
+NM_001031536	99..3497
+NM_001012804	68..2092
+NM_001006355	64..684
+NM_204172	65..1531
+NM_204212	1..2751
+NM_001348012	162..2225
+NM_204182	61..1314
+NM_204788	86..1264
+NM_001347945	34..1248
+NM_204471	162..3470
+NM_001006211	40..792
+NM_001318995	35..826
+NM_001322804	30..2675
+NM_001257371	191..829
+NM_001292086	17..1990
+NM_204766	50..5863
+NM_001318982	36..1613
+NM_001318432	1..969
+NM_001317736	78..812
+NM_001305110	67..969
+NM_001305109	71..973
+NM_001305111	63..740
+NM_001305112	64..597
+NM_001305089	1..3510
+NM_205501	87..1487
+NM_001293169	122..2614
+NM_001030587	20..1669
+NM_001293103	1..1086
+NM_001290554	77..2845
+NM_205054	17..1168
+NM_001277841	51..1013
+NM_001277715	58..930
+NM_001277631	13..933
+NM_001277630	13..1053
+NM_001271966	144..521
+NM_001271965	144..524
+NM_001271964	144..560
+NM_001113708	75..491
+NM_001271936	95..484
+NM_001271894	50..1765
+NM_205450	39..530
+NM_204650	3..245
+NM_205307	71..2014
+NM_001257373	16..1005
+NM_001128828	191..3520
+NM_001252284	300..881
+NM_001006305	30..788
+NM_001024456	6..2228
+NM_001242604	191..2770
+NM_001004378	103..1056
+NM_001201399	152..346
+NM_204992	88..282
+NM_001199613	1..498
+NM_001199429	179..2224
+NM_001195561	16..540
+NM_001195424	13..636
+NM_001111014	216..2867
+NM_001001775	216..2867
+NM_001167726	113..1909
+NM_001167759	22..1290
+NM_001167758	22..1287
+NM_001163651	189..1229

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gallus_gallus_RefSeq.fa	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,4595 @@
+>NM_001199713
+cccttcctcttccttcctcctcctcctcccccttccctccctgccccccc
+aacaccgaagggaagagacaattctcctccgagcagcagcaaacatgatg
+gcggcagctcccatccagcagaacgggactcacaccggggttcccataga
+cctggacccgccggactcccggaaaagaccgctggaagccccccccgaag
+cgggcagcaccaagaggaccaacacgggcgaggatggccaatattttcta
+aaggtcctcatacctagttatgctgctggatctataattgggaagggagg
+acagacaattgttcagttgcagaaagagaccggggccaccatcaagctgt
+ctaaatccaaagatttttacccaggtactacggagcgcgtgtgtctgatc
+cagggaacagttgaagcactaaatgcagttcatggcttcattgcagagaa
+gattcgagaaatgcctcaaaatgtggccaagacagagcctgtcagcatcc
+tacaacctcagaccactgttaatccagaccgcatcaaacaagtaaagatt
+atagttcccaacagcacagcaggtctgataatagggaagggaggtgctac
+agtgaaggctataatggagcagtcaggggcttgggtgcagctttcccaga
+aacctgatgggatcaacttgcaagagagggttgtcactgtgagtggagaa
+cctgaacaaaaccgaaaagctgtcgaacttatcatccagaagatacaaga
+ggatccacagagtggcagctgtctcaatatcagttatgccaatgtcacag
+gtccagtggccaattccaatccaaccggatctccttatgcaaacactgct
+gaagtgttaccaactgctgcagctgctgcagggctattaggacatgctaa
+ccttgctggagtggcagcctttccagcagttttatctggctttacaggca
+atgacctggtggccatcacctctgcacttaatacattagccagctatgga
+tataatctcaatacattaggtttaggcctaagtcaggcagcagctacagg
+ggctttggctgcagcagctgccagtgccaacccagcagcagcagcagcca
+acttgttggccacctatgcgagtgaagcctcagccagtggcagcactgct
+ggtggtacggcggggacatttgcattaggtagcctggctgctgctactgc
+tgcaaccaatggatattttggagctgcttctcccctagctgccagtgcca
+tcctaggaacagaaaaatccacagatggatcaaaggatgtagttgaaata
+gcagtgccagaaaacttagttggtgcaatacttggaaaaggagggaaaac
+attagttgaataccaggagttgactggtgcaaggatacagatctctaaaa
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+acaccagctgcaacccaggccgcacagtatttaattacacaacggatcac
+atatgagcaaggagttcgggctgccaatccacagaaagtgggttgagagc
+ccctgttaaacatgagattgttttaacccctccttaccctattttcaaga
+aggatgtactgtactttgcagaagtgaagtttttctgttattaatatata
+attatgcaaatgaatgcgactatgttgacaatgtgtatatgtaaatataa
+tgtgttttaccagatgtttcatagagagaattttttcttgatctgttttg
+ttctctatactttgcttgtgtatatttgtcagaggtgtttctagtgtaag
+atttaagcctgccattttaccagcattattgtagtttaatgattgaatgt
+agacagggatatgcgtatagttttcagtattagttctagataacactaaa
+ttaactactgttaggttgggtatggtggggtcagtgacctaaaatggagt
+gaggccaaagcactgtcatgtcagtcttacttcctgcttagggcacagtg
+aagtaggaaacaatattttgaaaataagttttaaaatttaaaatgatcaa
+aaagcaatatagttgcataaaagcactgtaaaatatttaaaaaggttaaa
+actgtggaaaattatattggtaagtttacagatcaataaaagcacctgtt
+ctccatctgaactagacaatggaaataatgctgcatgctggccatggccc
+attcttcaccatttgtaagttcaacaaaagttctcacatggagtcccacc
+tctaactgaggtttgtacatttgtttttaagcactgaaatcactactgat
+cccatcgcctggccagtagaacagtcattactccattaacattctcactg
+tttagacacataactgtggtacagtgtattggaaattttatatacaaaaa
+gtgaaagtgccaacaaattattgatagctgataatgtttcattatctgca
+actgcttgataagtatgttgcattttaagagcttataattgtgtataatt
+tgttaacactagaaacctattagtattgtgaatgtagattttactgtgaa
+gctatctgtgatttagctgtttgctcccatgaaggagtctttgcagcatg
+gcgctagcagccaatgcagtttctaatactcagtaatttgcatgttttgt
+ggagcatttttatgtcaccaaccagacagtatttcctgcatgcttattta
+gaagaggcagttttccttgagaggtagtggtctacctttgccaggctttt
+tgacaggtcatttcagagtaagcctttgttcccaagacccaacaactgtc
+accctcttctgtacctctcctgagtgccaactgcccaggccattgaccca
+ccatctgttaacctctgagtttgcccgctcaaggccactcataggggcat
+ccataaccaagcacctcctcatgctgtgcatgcagtcttaaattcaatgg
+acaaaaataaaatgctggctacctctggatcatctggctgagcaactgaa
+tttcaaaagagaattacttccatctcaacttcaacccattgattacgtcc
+atcctagcaagctaaatggcatcccagctgctcctttctgtgcaaccaat
+taaagaacaatgagtgtgatgctccatgtctgaatttcgtccagcctctc
+tctgaactgtgatctttgtcctcatgaactttcccttttgttcattgaac
+tatatggactcttcatttcatattgatttactgtgcaatttacttttgga
+cattgagaacttgaaataattccctgatcccttcccccttcactattaat
+aactcatttctgtcaaactgtaagagtagactcattttttttagttttta
+acattggattgttatttcatttagagttctctatctctaaatatttaatt
+tagagaatgattaaaaagggaatgatatgcttgtttaaaatgaaagagaa
+aagctgtagtaaactgtgttacttggtaatgactatttatcgtcgatact
+ctgtagctgtgtaagttttgacaaatagtgtatctcgtgaaatcagtggt
+tagcattgccgctattatatttactcattttatcattataaatgtgctta
+gttcatcatgtag
+>NM_001199712
+cccttcctcttccttcctcctcctcctcccccttccctccctgccccccc
+aacaccgaagggaagagacaattctcctccgagcagcagcaaacatgatg
+gcggcagctcccatccagcagaacgggactcacaccggggttcccataga
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+tcttccccaactaccaccaagtcctctccatctgatcccatgaccacctc
+cagagccaatcaggtaaagattatagttcccaacagcacagcaggtctga
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+ttatcatccagaagatacaagaggatccacagagtggcagctgtctcaat
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+atctccttatgcaaacactgctgaagtgttaccaactgctgcagctgctg
+cagggctattaggacatgctaaccttgctggagtggcagcctttccagca
+gttttatctggctttacaggcaatgacctggtggccatcacctctgcact
+taatacattagccagctatggatataatctcaatacattaggtttaggcc
+taagtcaggcagcagctacaggggctttggctgcagcagctgccagtgcc
+aacccagcagcagcagcagccaacttgttggccacctatgcgagtgaagc
+ctcagccagtggcagcactgctggtggtacggcggggacatttgcattag
+gtagcctggctgctgctactgctgcaaccaatggatattttggagctgct
+tctcccctagctgccagtgccatcctaggaacagaaaaatccacagatgg
+atcaaaggatgtagttgaaatagcagtgccagaaaacttagttggtgcaa
+tacttggaaaaggagggaaaacattagttgaataccaggagttgactggt
+gcaaggatacagatctctaaaaagggagaattcgtacctggcacaagaaa
+tcgcaaggtaaccattactggaacaccagctgcaacccaggccgcacagt
+atttaattacacaacggatcacatatgagcaaggagttcgggctgccaat
+ccacagaaagtgggttgagagcccctgttaaacatgagattgttttaacc
+cctccttaccctattttcaagaaggatgtactgtactttgcagaagtgaa
+gtttttctgttattaatatataattatgcaaatgaatgcgactatgttga
+caatgtgtatatgtaaatataatgtgttttaccagatgtttcatagagag
+aattttttcttgatctgttttgttctctatactttgcttgtgtatatttg
+tcagaggtgtttctagtgtaagatttaagcctgccattttaccagcatta
+ttgtagtttaatgattgaatgtagacagggatatgcgtatagttttcagt
+attagttctagataacactaaattaactactgttaggttgggtatggtgg
+ggtcagtgacctaaaatggagtgaggccaaagcactgtcatgtcagtctt
+acttcctgcttagggcacagtgaagtaggaaacaatattttgaaaataag
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+gtatttcctgcatgcttatttagaagaggcagttttccttgagaggtagt
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+aactgcccaggccattgacccaccatctgttaacctctgagtttgcccgc
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+tctgaatttcgtccagcctctctctgaactgtgatctttgtcctcatgaa
+ctttcccttttgttcattgaactatatggactcttcatttcatattgatt
+tactgtgcaatttacttttggacattgagaacttgaaataattccctgat
+cccttcccccttcactattaataactcatttctgtcaaactgtaagagta
+gactcattttttttagtttttaacattggattgttatttcatttagagtt
+ctctatctctaaatatttaatttagagaatgattaaaaagggaatgatat
+gcttgtttaaaatgaaagagaaaagctgtagtaaactgtgttacttggta
+atgactatttatcgtcgatactctgtagctgtgtaagttttgacaaatag
+tgtatctcgtgaaatcagtggttagcattgccgctattatatttactcat
+tttatcattataaatgtgcttagttcatcatgtag
+>NM_001030697
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+gatgggcagggggccccggcggctgccgccctccaggagatgaattaaaa
+tgcagcacaccacgtgcacagaggacaggatctatcatgcactggagaga
+tgtctgcacgggcttagcagagatgctgtctccagcagatgggctgcagg
+gctgtgcctgaactgctggagcctgcaggagctggtgagcagggatgcag
+gtaactacctcatcctggtggagaaaatcctcggcaaggccagggaggtg
+caggagaagtgtgactacgacctggtgatgcccctggccctgcttttcta
+ctacgcggtcctctatgctccccacatcccaccagactccgagctgctcc
+tgaaagctgccagcatctaccacagcttcctcacctggcccgtgccctac
+tgcgacgtcttccgtgagctgctcaccttcatcagtgatgagctcaaggc
+gccagggatttccttccagaggttggtgaggacggagcaggggctgcctg
+tgaagaactaccagagctccactgtgacggtgctgctgctgaaccgctcc
+gaggtgcagagtgagttcctctccatcgcagagaagctgagcagcactga
+gcccccccggcacgccacgctcgtcctgctgctggagcacctctaccagg
+tcaccttcggcacccgctgcgacctgggcagcctgcaccacctcctgaag
+gccaagacactggaagagctctctgagatctacaccagcgctgctgaagc
+gcaggagatcgcagccgccagcagtgaccctgtgttggcccgggagcggc
+tgcagagcgctctgcgggacattgccggggcagcagcacttcctaccatt
+gcaggagatgcgcagccccgcaggctgcagcccatccccatccctacttc
+gcgctgctacacctacagctgggaccaggataactttgatgtcctcaatg
+atgtcctcagcaaggagtgcagtgttgttgagcctgtggcctcagagaat
+gaggaggacgaggaagaggaggaggaggatgtggaaacagacggctgttc
+cccagagagggactcgctgctgtcccccatctcctccatttccaaggact
+ccgtgtactcagcgctgtcagaggatggacccaagcactcctgcgtgtcc
+ctcttcagcagctccaaggactccatctcagagctgacggtggtctccaa
+gaagtccttgaggtcttttgtctccagcctgaaggactgcatggacagcg
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+gagctgaaggtggagaagacccaccacaaatacagacacacgctgaccaa
+caagatctacaagctcttcaagagcaaaagccagctggtcctgaggagag
+acctgaaggactgtgtggatacaggctcgctcccactgcgccgtgctgag
+agcctgtgccacccccaggccaagccccgcatcccggcacgctcccggcg
+cgctcactcattgccacagcacgggctgggccagaagctgcagaccccgc
+agaccccgcagctgctcagcctgccccgccggcccttcctcagctacgac
+gaggatgccaaagtggccaccatgcgcgtggtggtcttcggctccgaccg
+catctcagggaaagtagcccgagcctacagcaacctgaggctgaaggaga
+gcacctgccctacactgacaaggtacttcaagctgcagtttttctacgtc
+cccgtgaagaggagctgcctgctgccagcagccctgctgatgcatcctcc
+tccatccccaagcgacctgcagctccgcgccttggcacaggcggagccca
+ccttggctggggcggagagcagcaccaatgacatctcccactacatcggc
+atgttggacccatggtacgagcggaacgttctggggctgatgaacctgcc
+catggatgtcctgtgtcagtctgccaagcctgaggctgagccccaggagg
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+g
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+>NM_001167726
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+gaaaagctggtatcttcagaagggtcaaattttcaataattcacagggtt
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+cacctaacatttatgttttattcaacttgcttgaaagatttaggtttctt
+accctctttcgcataaaatatttttctcctaaaacaaaatcatgcattga
+ttttttttttctatatttcaccgcattccatttgctttcaaggcaaattt
+actctaaagaaatttaatgactatgtcattgttagatatgttttaaagac
+cggaaggtttgagtttttaaatagtccagctctcttgtaaatgcatcact
+gcacaaaagaatgagcagaaagtaaggacttctctgcacttcatcccaag
+tgcactattttaaatgataaaaccctgttgctttaggaatggagcatgct
+gttatttctctggaatttgttttttttctttgtgtgtgtgtgtgtgtgtg
+tgtgtagccatgatgtgcattttattttgaactgcagaaatgtattgagc
+cgaagcacctacctggtccttcctcagatggcccagcagtttcctgctat
+gcaagtgactgctgaagggctcaggtctggctccctagcacccctcacag
+gaggaggtgaaatgcagcccactcccagtgcgttgtatgaacagtgtgag
+gctgttccaatcagtgtcaattaaaaacagcctccagtccgcggtatcaa
+gaaccagaacttcctctcttctgctagcttcccagtctccactctgaggc
+ctgaggtgtgagatgtccagtgacacctcgcataggtatctggctaggta
+aggcactcaagtctgcattatagggctttgctattttattactaatgtac
+gaagcaacacagcaagaaacatactggtgtatttatttatacagctggtt
+attgtggcagataaggcttaagaaccttatttttactgtctggctatcta
+aaaatgcaccctggaaaaaagcaataaatagcacacttggatacataggg
+aacagaaaccgcaaccacaagacaaaaagccacttgagatgtacagtcat
+ataccagatagaaaggaactccaaaaacctccgtggtttaagggaaagca
+gtaattactcaaatgcagtaattcactgcatgcagagcaatgaggtgctg
+cagctgtaatgcattatatcaattacacgggtctgacagaatgggctctt
+ccacactgtacaaatgaagtcaggaaaactgttccctgtaaccccatgta
+cccaactccacacagcagtttttcctcacttctgcagcacacctttccag
+aagcatgaaagagatacagagaacgcttgcaatgtgtcgtttattcagtt
+cttccttttaagttctcaatgtttaagtttattgaatgtaaacattttct
+ttatagaaggctctttatagcacaatttgtttttacagtataattaaata
+ttttcaaaattctgtttttctttgtaaacaagttggtttggtaattaaag
+aactggttatactgaa
+>NM_001167759
+cggcccggcctgacccaggggatgcctgaaaggcaagggaaggacagtga
+aagccatgtcagcagcagctgtaccagcaccagcaactcagttgcttgct
+ttggacagtatcaatatacagcaaatgaatatcaagccatccagcatgct
+cttcgtcagaaactgggtccagagtatatcagcagtcggcaagctggggg
+aggacaaaaggtctgttacattgagggtcacaaggtaatcagtctggcca
+atgagatgtttggcttcaatggctgggctcattcagtcactcaacagaat
+gttgactttgttgatctcaacaacggcaggttctatgtgggggtctgtgc
+attcgtgaaagtgcagcttaaggacggctcataccatgaagatgtgggct
+atggagtcagtgaaggcttgaagtccaaggccttgtccttagaaaaggca
+agaaaggaggcagtaacagatggactgaagagggcgctcaagtgctttgg
+gaatgctcttgggaactgcatcctagacaaagactacctacaagcagtta
+ataagcttccacgtcagatgccccctgagttagatctggtgaaaactaaa
+agacaggactatgagcctgaaatagagaaagcaaggtacgacggctgttt
+ggaaaggcagaacccaggatggagacaacagtgtgaaacggcaccaactt
+gtaagcccactcacacagaggcttccggagtgacagaagatcagaagcag
+ccaagcagttctggaaatacagattccccagctgttgagtgtgatgccac
+gtatcagcggaaactgcgacaaaagcagctgcagcaacagttctgggaac
+agatggaaaagagacgtcaggttaaggaagttactcccagcagcaaacag
+gcaacagccaatcctcctgtaaaacacagcactccggcagcagtacagca
+ggaactggcaatagaagaagagttctttgcagatgatcttgaactctggg
+acatttccttggagaccaccgaccttaacaagttgatgtgtcacaaagca
+gcaggctcaccagcagcacagcagccccccgagacgccccacagacgtca
+ccagatgacaactcgtaacaggacgcctcagagaatgcattatcacaaac
+cgcctgtgaggtttgcacagttgcagccatctgctgctctcacaagcaac
+agccacggtgccaaccaacgcacaccagcagagcacagcccttacaggag
+aagtcaaagctggaagaagcggaggctagaacccacataggacacgtggt
+ggcatcattacctacatgctggattacatcataagactgcagttggctgc
+tcaaagtacgtgaggaagcttcatctattaatagattgtcctaaagcaac
+acagaatagccagagagacacagccagcaagaacttcatgtgctttgggt
+ttattacatagtccagatttttttttctataaacacacaatcatttgtgc
+tcctgcacaactcgtggctgttttacaaataatttgcctgagaattgtag
+cataagtaaaccttcaaatgagatgccatagcttcttccctgctcagtgt
+tgcatttaggcgtacagaaaagtttttttccaataaaacgaggacagggt
+gggctgtggccccaggaaagcacactgaccgcagtctcccattccctcgg
+gccgtttgcagctgtggcagcctctgcctcacatgcagcacggctgcctg
+cccagaggctgcacaagcaggggcagagcattgccctgacacggctctgc
+ctcacctcaaccctcaagcacgcggcattcccagcagcagcagcagcaca
+tccacctgtgcccacgcagcacggggtcaggaacacgcggggactgctat
+tgaggggtacatacagcatctaagtgctggtttggaccttttgtgaaatg
+aatgagagctgcaatcttatacttttagtgttttaaatcagcttttactc
+ctttttaacacaagaataaacactaaatgtggacagacaaa
+>NM_001167758
+cggcccggcctgacccaggggatgcctgaaaggcaagggaaggacagtga
+aagccatgtcagcagcagctgtaccagcaccagcaactcagttgcttgct
+ttggacagtatcaatatacagcaaatgaatatcaagccatccagcatgct
+cttcgtcagaaactgggtccagagtatatcagcagtcggcaagctggggg
+aggacaaaaggtctgttacattgagggtcacaaggtaatcagtctggcca
+atgagatgtttggcttcaatggctgggctcattcagtcactcaacagaat
+gttgactttgttgatctcaacaacggcaggttctatgtgggggtctgtgc
+attcgtgaaagtgcagcttaaggacggctcataccatgaagatgtgggct
+atggagtcagtgaaggcttgaagtccaaggccttgtccttagaaaaggca
+agaaaggaggcagtaacagatggactgaagagggcgctcaagtgctttgg
+gaatgctcttgggaactgcatcctagacaaagactacctacaagcagtta
+ataagcttccacgtcagatgccccctgagttagatctggtgaaaactaaa
+agacaggactatgagcctgaaatagagaaagcaaggtacgacggctgttt
+ggaaaggcagaacccaggatggagacaacagtgtgaaacggcaccaactt
+gtaagcccactcacacagaggcttccggagtgacagaagatcagaagcag
+ccaagcagttctggaaatacagattccccagctgttgagtgtgatgccac
+gtatcagcggaaactgcgacaaaagcagctgcagcaacagttctgggaac
+agatggaaaagagacgtcaggttaaggaagttactcccagcagcaaacag
+gcaacagccaatcctcctgtaaaacacagcactccggcagcagtacagca
+ggaactggcaatagaagaagagttctttgcagatgatcttgaactctggg
+acatttccttggagaccaccgaccttaacaagttgatgtgtcacaaagca
+gcaggctcaccagcagcacagcagccccccgagacgccccacagacgtca
+ccagatgacaactcgtaacaggacgcctcagagaatgcattatcacaaac
+cgcctgtgaggtttgcacagttgcagccatctgctgctctcacaagcaac
+agccacggtgccaaccaacgcacaccagagcacagcccttacaggagaag
+tcaaagctggaagaagcggaggctagaacccacataggacacgtggtggc
+atcattacctacatgctggattacatcataagactgcagttggctgctca
+aagtacgtgaggaagcttcatctattaatagattgtcctaaagcaacaca
+gaatagccagagagacacagccagcaagaacttcatgtgctttgggttta
+ttacatagtccagatttttttttctataaacacacaatcatttgtgctcc
+tgcacaactcgtggctgttttacaaataatttgcctgagaattgtagcat
+aagtaaaccttcaaatgagatgccatagcttcttccctgctcagtgttgc
+atttaggcgtacagaaaagtttttttccaataaaacgaggacagggtggg
+ctgtggccccaggaaagcacactgaccgcagtctcccattccctcgggcc
+gtttgcagctgtggcagcctctgcctcacatgcagcacggctgcctgccc
+agaggctgcacaagcaggggcagagcattgccctgacacggctctgcctc
+acctcaaccctcaagcacgcggcattcccagcagcagcagcagcacatcc
+acctgtgcccacgcagcacggggtcaggaacacgcggggactgctattga
+ggggtacatacagcatctaagtgctggtttggaccttttgtgaaatgaat
+gagagctgcaatcttatacttttagtgttttaaatcagcttttactcctt
+tttaacacaagaataaacactaaatgtggacagacaaa
+>NM_001163651
+gagactccgtcggaatcggtgctccggggagagctccgcagcttttcctg
+gctgagctatacttgaagcgactgaacttggcaggagctggggcttaaag
+cagcaccggagctgggctggtttcttcccaacttgtctgagcaagagcag
+gtgctttggagcaacgagagctgcggtgcggctgtgccatggcagcggtg
+gtggcagagaagctcagccgcctcttcatcagcgtgcgccaggtccccca
+gctgctggcccccccggtgcccaccaccgtcagcagctccgaggtgccga
+gggttttctggaagccttacatccacaccggctaccgcccggtgcaccaa
+acctggcgctattacttctcgacgctcttccagcaacacaacgaagccat
+caacgtgtggacccacctggtggccacgctgatcctgctgctgcgcttcc
+agcagctctcccagagggtggattttgggcaggacccgcacgcccagccg
+ctcctcatcatcatcacggcatccatcacctacctgacgttcagcacgct
+cgctcacctcctgcaggctaagtccgagttctggcactacagcttcttct
+tcatggactacgtgggggtggccatctaccagtatggcagtgctctggtg
+cactactactatgccatcgagcccagctggcacgagaagatccagggctt
+cttcatgcccacagctgcgctgctggcctggctgtcgtgtgcaggctcat
+gctacgccaagttccgctaccatcagtcagcagggctgctgggccggctg
+tgccaggagatgccctcaggcctggcctacctgctggatatcagccctgt
+tgtgcaccgcatctgcaccgcatcacctgcggagcgcacagatccggccc
+tgctgtaccacaagtgccaggtgctgttcttcctcatcggtgcctttttt
+ttctcccatccttacccagagaagttgcttcccgggaaatgctacttctt
+tgggcaaagccatcagatcttccatgtcttcctggtgctttgcactctgg
+cacagatcgaggccgtggtgctggactatgagtccaggcggcacatctac
+tcctcgctgcagggtgacctggcgcaccacttctctgccctgtgtgtctt
+cactgtgacctgctccgtgctcacggctgcatacatggcacggaaggtga
+gggacaaactgagcttcaaagaagattgagatttggggcagagtggggga
+taccatggccaaagctgcatgctccaagga

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amaVit1_Gallus_gallus.psl	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,12 @@
[phone]	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,
[phone]	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,
[phone]	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,
[phone]	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,
[phone]	+-	NM_001292086	6644	481	731	LMAW01000003.1	4188689	2832850	2833124	2	110,140,	481,591,	1355565,1355699,
[phone]	+-	NM_001292086	6644	508	782	LMAW01000003.1	4188689	2832901	2833151	2	102,148,	508,634,	1355538,1355640,
[phone]	+-	NM_001292086	6644	562	679	LMAW01000003.1	4188689	2832851	2833151	2	43,74,	562,605,	1355538,1355764,
[phone]	+-	NM_001292086	6644	619	679	LMAW01000003.1	4188689	2833085	2833145	1	60,	619,	1355544,
[phone]	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,
[phone]	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,
[phone]	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,
[phone]	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,

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.bigpsl	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,12 @@
+LMAW01000001.1	517465	615765	NM_001012804	1000	-	517465	615765	0	18	139,137,107,81,142,58,94,3,171,39,114,150,87,2,112,74,32,119,	0,5531,10924,11277,14625,16705,17663,21512,21597,27451,32690,33190,43784,44910,44925,57174,98049,98181,	121	2062	-	4592	2530,2669,2806,2914,2995,3137,3195,3289,3292,3487,3721,3844,4036,4123,4125,4246,4320,4352,			10443977	1247	370	0	44
+LMAW01000001.1	9729332	9765132	NM_204766	1000	+	9729332	9765132	0	8	108,153,66,93,39,171,99,84,	0,4809,21687,25888,32710,33223,35333,35716,	262	2188	+	5992	262,388,574,688,1414,1459,1981,2104,			10443977	537	234	0	42
+LMAW01000001.1	10027590	10064141	NM_001006176	1000	+	10027590	10064141	0	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,	0,3564,3763,3927,5671,6106,6864,8056,15894,16204,32078,32234,32383,33208,33389,33675,33897,34150,34357,34553,34775,34994,35153,35411,35598,35793,36026,36216,36524,	296	3230	+	3248	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,			10443977	2134	377	0	62
+LMAW01000002.1	103604	131424	NM_204766	1000	+	103604	131424	0	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,	0,803,4160,4305,4398,4629,4653,5657,8443,9363,9432,9544,10653,10787,11262,12579,12834,12989,13304,14163,14426,15078,16515,17068,17725,18581,19120,19914,20341,20845,21300,22189,22294,23186,23801,23939,24113,24451,25634,25838,26157,26416,26650,27499,27733,	49	5815	+	5992	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,			5883884	3724	1107	0	326
+LMAW01000002.1	3610886	3618513	NM_001031013	1000	+	3610886	3618513	0	5	33,66,21,276,138,	0,69,7055,7213,7489,	69	702	+	971	69,138,232,285,564,			5883884	420	114	0	0
+LMAW01000003.1	259524	268833	NM_204766	1000	+	259524	268833	0	5	27,80,11,66,36,	0,1731,2005,2855,9273,	574	1453	+	5992	574,700,780,847,1417,			4188689	143	58	0	19
+LMAW01000003.1	2559457	2573393	NM_204766	1000	+	2559457	2573393	0	5	84,66,33,13,66,	0,3787,3892,11310,13870,	553	1588	+	5992	553,739,844,1457,1522,			4188689	189	73	0	0
+LMAW01000003.1	2820233	2835138	NM_001292086	1000	-	2820233	2835138	0	37	27,162,54,12,11,18,45,15,93,29,26,161,23,21,106,70,125,72,9,34,23,90,69,90,72,93,171,137,135,93,87,146,90,5,107,727,64,	0,100,289,415,466,601,625,753,805,1069,1098,1190,1352,1546,1601,1712,1782,1910,2192,2202,2337,2841,3036,3121,3302,6920,7314,7796,8505,8919,9349,10865,11395,11653,12233,12598,14841,	10	5375	-	6644	1269,1369,1559,1691,1751,1884,1911,2026,2075,2352,2382,2475,2636,2829,2891,2998,3074,3206,3565,3574,3703,4204,4412,4505,4687,4759,4856,5043,5180,5315,5408,5495,5641,5731,5736,5843,6570,			4188689	2710	404	0	198
+LMAW01000003.1	2832850	2833124	NM_001292086	1000	-	2832850	2833124	0	2	140,110,	0,164,	481	731	-	6644	5913,6053,			4188689	200	50	0	0
+LMAW01000003.1	2832851	2833151	NM_001292086	1000	-	2832851	2833151	0	2	74,43,	0,257,	562	679	-	6644	5965,6039,			4188689	92	25	0	0
+LMAW01000003.1	2832901	2833151	NM_001292086	1000	-	2832901	2833151	0	2	148,102,	0,148,	508	782	-	6644	5862,6034,			4188689	182	48	0	20
+LMAW01000003.1	2833085	2833145	NM_001292086	1000	-	2833085	2833145	0	1	60,	0,	619	679	-	6644	5965,			4188689	49	11	0	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_both.bigpsl	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,12 @@
+LMAW01000001.1	517465	615765	NM_001012804	1000	-	517465	615765	0	18	139,137,107,81,142,58,94,3,171,39,114,150,87,2,112,74,32,119,	0,5531,10924,11277,14625,16705,17663,21512,21597,27451,32690,33190,43784,44910,44925,57174,98049,98181,	121	2062	-	4592	2530,2669,2806,2914,2995,3137,3195,3289,3292,3487,3721,3844,4036,4123,4125,4246,4320,4352,	ggttcggcggccgccggacggttgcgtgacgaggcgggcagatccttctggatacgagcggagagccatggccgacgtgttcccgggctccgagcccggcgcggccccggacgcggcgcggcgctttgctcgcaaaggggccctgaggcagaagaacgtgcacgaggtgaaggagcacaaattcatcgcgcgcttcttcaagcagcccaccttctgcagccactgcaccgacttcatctggggatttgggaaacaaggatttcagtgccaagtttgctgttttgtggttcataagagatgccatgagttcgttaccttctcctgtcctggagctgacaagggacctgacaccgatgaccccaggagcaagcacaaatttaagatccacacctatgggagcccaaccttctgtgaccactgtgggtcccttctttatgggctcctacaccaagggatgaaatgtgacacttgtgatatgaatgtgcataagcaatgtgtgataaacgtcccgagcctctgtggcatggatcacactgagaaaaggggaaggatttatctgaaggctgaagtcactggtgacaaactggaagtaacagtgcgagaagcaaaaaacctaattcccatggatccaaatgggctttcagatccttatgttaaactgaaacttatcccagatcccaagaatgaaagtaaacaaaaaacaaaaaccttccgttctaccctgaatccacactggaatgagtcattcacatttaaattaaaacctacagacaaagatcgacggctctctgtagaggtctgggactgggatcgaacaaccaggaatgattttatgggctctctttcatttggggtgtcagagctcatgaagatgccagccagtggatggtacaagctgctgaatcaagaagaaggtgaatattataatgttccaattccagatgctgacgaggatggaaatgcagagctccggcagaagttcgagaaagccaaacttgggccagctggtaacaaagtcattactccatcagaagacaggaattcaagtgtgccatccaacaatctggacagggtgaaactgacagatttcaactttcttatggttcttggaaaaggaagctttggaaaggtgatgctggcggacaggaagaatacagaggagctctatgcaatcaaaatactgaaaaaagatgtggtgattcaggatgatgatgttgagtgtacaatggttgaaaaacgagtgctagcactgcaggataaaccaccattcctgacacagcttcactcatgtttccaaacagttgaccgcctgtattttgttatggagtatgtgaatggtggggatctcatgtaccacattcagcaagtaggaaaatttaaggagccacaagcagtgttctatgcagctgagatctcagttgggttattctttctccataatagagggattgtttatagagatctgaaattggataatgtgatgttggattcagaaggacacattaaaattgctgactttggaatgtgcaaagaacatatgttagatggagtaacaaccaggaccttctgtggcaccccagattacatcgcaccggagatcattgcttatcagccctatgggaagtctgtggattggtgggcatatggagtgctgctctacgagatgttagctggccagcctccatttgatggagaagatgaagatgaacttttccagtccataatggaacataatgtttcctatccaaaatcgctgtccaaagaagctgtctccatctgcaaggggctaatgactaaacatcccgcaaagcgccttggctgcggcctcgaaggtgaaagagacatcagggaacacgctttcttcaggagaattgactgggagaaactggaaaacagagagatccagccacctttcaagcccaaagtgtgtggcaaaggtgctgaaaacttcgataaattcttcacgcgaggacagccggtgttgaccccgccagaccagctggtcattgctaacatagatcaatccgattttgaagggttctcctatgtcaacccccagtttgtacatcccctcctagaaaatgtagcatgaaacagcagaacaggaacaaatcccgcagtggggaacggttcttaaccctaaaatttttaggtttttgccttgattccgtttgggcctgaaaattatagggttagaaagtgtaagatgggagaaaggccacttagtgaggattttgactttgcaaccaaaacgtcttaatgggagataaattagcatacagtgcccatttctcctactagaagtcaccatgactcgtctgaagttccccatttttggtacattctgtagttctgtagctccccgctgtccttttgctccgtttttcactccgctgctgttacaaataatccaagacccgacctgagaagcacctccagtactcagtccttgcaggggaccagctccccgctcctatgggcaccatggggagagcagcgcacgggactggagagcgccggggaggagaggcattgcagaatgtggtggaaagcagttgttaccaaaacccgacaaataaatacgagttgggagtgggagggcaggggggatgaaatcctattagagcccaaagcttcgtgaaccaatcctgtaagcaacaccaaatttaaacacgctccggcagtggccagatctctagatctttgctaagtagcatgtgataaactcgagggtgaagttttgtctttaataataataataatagtaataattttaataatatttttgtgaattttaatctccgtgagattattctgtgatccagggtgccattgtttgttcagttgatttcatttgcaccactcctcaagctcactgttgactggttctaataacaccaacgttttactatgagatttgttaacctggaatgtaaaacagaactgtaatcccttacatcttatttacttgtgtgtgttgtagtctgcagtatagggcagtaaattgaaggaagtattgtgtatgctaaattaacaaaaacgcagtcccaggtgactccctgatttttccagaacaactcatgaaaatgaattgagatttagttctacagtaatcaattctaactcagaaaacttggggctgtacaataaccaagcttgaaagaagcacctgaagcttgttttattggcagaatggaatttaacacattttacatacgcttcatgcaatgaattttgcatgtttagtaataactcttaataataagagttaataataagcagttctatattgacattaccatatcaagcatacagagtattacaaaagttttataaaacaaattgtgctttatttgtggaagtacttgttctgaacgacatcatttaggtttagctcaatgttttcttgctgttgttttgggttgtttttttctagtttttggatattgttaatgacttagggtatcatctgtttttttaaacgtagatctacttttaaacaataattgctacctgcaggttttatacaagtttcaattaggcttttgtttcatgtctgctgattactgacagggaaagaaatagattttatttgcaatgatgaacgctgtaattaatgcaatcttctcctctcctatctcacttagatacaaattttgatatttcctcttaccaacttaccagaagatcttaattcaaatatcagtaaatatttttgtgcttactttggttttgttacagcatgtaaaatagtaggcggtgcgttttccttttcttcccttcagcctcgttaatggtagcagccataggcactctttgtctgtcggatgtgcatgatgatgccagaagcatgatgtctctgttgctgcatgcagactgaatacagtttttccagcatgtaaacatattcaaaaagtcagatatttgccataaaagacttacatttatactagaatatgtaaccggagggtgggggtgggagcggggggggaggaatctactttctaatcatcttttattacaataaaacattgagcctgtgccaaagattctgctagaaagatccagtcctgcagattggacggcgatgatgtgcaggagtgaccccgtggcacatgggacagttggtgagcgaaccgcagctggatgtgagcagaagcggccgtgcggtgctcctgcaccacggatgccttccaaagccgtcctttggcgcctgggatttgcagcactccagttgtgtgaccagccctgcttcctttgtggtcacagccctaaggttggagcatccccagagagggctcagcccgtgttggatggacccggcgctgacacatggcatcccccaacgaacagctccccagattgttgcctaaataaacagaactcaaacattttaatacattttaggagtacagtttttcaactatccggtgtcagatatgttatcagccaaatttgggcattcgttttcctctttgtgtattatatacctgaagattatggtatgttgttccccataaagcatgtggactagtgcagcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaa	68..2092	10443977	1247	370	0	44
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ctcagtaagttggcctggtcatgaggacatcaggggatatggcagaaggatgctctctttggcagaggtgtaaacttttacttgactgccttttgaaaacttagcttgaccctgcagaaggtagttgatagttttctactgctgtagctgcctcagctggcacactggtgtgtcggttgtgactggaggtggtgcaagaggtagaacaggacagttctgtgtgtggcagcaagttttaactcggctcagatgtgaaactgcagccacaggaatgtgttaaacatgagatggtgactttccagtgaagtcataggtatttatttctcagccagtgggcataggagcccatggtgtcggcccattctaatggagtgcttttctctaacagcttaatgctgctggtcaagctgagtgttactgagtgcatagagatggtcacatgggaaagaaagagagaattttgtttctgataaatgttcttttaatattagttataagaagttttacatattagatttgtgaaattcagctacgctgttgtaacacttagacacttgcctgtggcttgacttggaagtgcttgtggagagcaatgtgactaacacctcgtgttgcctagtgatgccctttcacttgagctggggtttttttagtgcctgtctggacatgaaagacttagagaaaagctgcaaacaagtgttgactgctagcttgtatctttaattgctttaaaactcgtgggcattctcatgaattatataagcttaagtagttgagaaaatgacataaaattaagtaaatccctgctgaaatcattctcagacagaatttgacaaaaaaaaatcctttcacaagtcttttttgacattttttttctaaaggattttttatggtttcaagactggactgatgcttggggggaaaaaggagttactgaagtggaagcttaactagaaagtttttatttgttgctttgttttctccattatttcgtgaagaattgagagactgtagagccagtttaccaacaaaagtaacctcatgtcttttgagttaggatgaaattttctgggaaagaatggcattcctgcagttattgatagccatggaatcatatatacactgtattcttcatatattgtcaattaaacataaataaaatcctaggaaatggtaaaagcatcaactatcacaccctcttttttctatcttatgactgaattaactttctgtgttttcatgcttttctcctcaaaacacttcataatgtaactggaaaagacacactaatcctagcgtgatgatctgtcagttaccttgtgggttttttcctctttgtctgtcagtgtaaaggtgtatgatagacattctgtacagaacgggctcttagaacaggatttgctgttgagctctacagtaaaccttttattttaattttgcatggatgctcaaggaccactctcattttcatatgtaaaggaaataaacttacgtttttggcaacggcagtaatcagcatctttccttcaggtgtttagtacacttgtacatagtgatcgtgtttgggaagttgtcctgcttggttggctgagggttgtattgtgagatgtgtaacctactatctctgtaagcccagtgctgttgctcgttgtatttaatgccagcagcatcaagttttgtttacaaatccggaatcaggtaactgtatttaaactatgtcagcttgtcatctcccagtcttatttttcagcttaaa	17..1990	4188689	92	25	0	0
+LMAW01000003.1	2832901	2833151	NM_001292086	1000	-	2832901	2833151	0	2	148,102,	0,148,	508	782	-	6644	5862,6034,	ggcgcgtgcagcagccatggccgacatggaggagctgttcggcagcgacgccgactcggaggccgagcagaaagataccgattccggctcagactccgactctgaccaggagaacgcgggctccggcagcaacgcctcgggcagcgacagcgagcaggacgacgagcgggaggcagcaaagcccagcaacaaggagctgttcggagacgacagcgaggatgaaggagcctcccatcacacgggcagcgacaaccactccgagaggtcgtacaatcgctccgaagcttcggggcactctgagcacgaagacaacgatcagtcggacgtggaccagcacagcgcttcagaagcggctcatgacgatgaggaggacgagcgggggcacggctctgatgagggcagtcaccattctgagggagatggttcagaaaaggcccattcggaggatgagaagtggggcaaggaggacaaaagcgatcagtcagatgatgaggagcgacagcagaactctgatgatgaggagagacagcagaactcggacgatgaggagaaagcacagaactctgatgaagatgagaggccgcagatgtctgacgatgaggagaggctccagaactcggatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggagaagatgcaaaactcagatgatgatgaaagagcccagcactctgatgaggagaagatgcagaactctgacgatgacgaaagggcccagcgctccgatgaggaggagcaggagcataaatctggagagtctgcaagaggcagcgacagtgaagatgaagtcctgcgaatgaagcgaaagaaaccaattgcatcagattcagaggcggacagtgatacagaaggccagaaggaacacgcagacgtcatggacctgtttggaggagcagatgacatttcttcgggaagcgatggggaagacaagccgccaactccaggacagcccattgatgagaatgggctgagccaagaacagcaggaggaagagcctattccagagacaagaatagaggtagaaataccaaaagtaaacacagacttgggtaacgatttgtattttgtgaagctgcccaacttcctcagtgtggagcccagaccatttgatccccagtattatgaggatgaatttgaagatgaggagatgcttgatgaggaagggagaacgagattaaaacttaaggtagaaaacacaatacggtggcggatgcggcgagatgaggaagggaatgagattagagaaagcaatgcccggatagtcaagtggtcggatggaagcatgtctctccacttgggaaatgaggtctttgatgtgtacaaggcaccgctgcagggagatcacacccatctgtttatcagacaagggacaggtctgcaaggacaggctgttttcaggacaaagttaaccttcaggccacactctacagacagtgccacgcacaggaagatgactctgtctctggcagataggtgttcaaagacccagaaaattcgtattttgccaatggcgggtcgtgatccggagtctcagcgcacagaaatgattaagaaagaagaggagagattaagagcttccattcgcagagaatctcagcagcgaagaatgagggagaagcagcatcagcgtggtctgagtgctaattacttagaacccgatcgctatgaagaagaggacgagggagacgatgcgatcagtctagcagctatcaaaaacagatacaaaggtggcatcagagaggaacgtgctagaatctattcttcagacagtgatgaaggctcagatgaagataaaacacaaagactactcaaggcaaagaaacttactagtgatgaggaaggggagccttctggaaagagaaaagcagaggatgatgacaaagcaagtaagaagcataagaagtatgtcatcagtgatgaagaggaagatgatgatgattaacattgagggagcactgaagttgctttctatatatacatatttatatataaattgtacagttctcttacagcaaagatgtaagtagccatattggggttattttgataaaggagaattccattgaaatttgtgtttctggtgtgaataaaagttggtttctttctttttactttctcatatttttacatcttatcttactgcagcagctgctgcaatggggatcatcatagcatcagtttttaaatcttgtacagtacatttcagttttgaaatctatagtacaaactggttgtacaactgaatagaactgaataaatcagtggtcttactgagttcattaggagaaatcataatcttcatatagaatgcttaaattataagttttctcagccaggttatggagatgaaggttaccatttgtacagaagatttggaatatcatatgagtggcacaacaccgtactgttttttcctgcactttcctattacgtactgctggctgtagatggtacattactgtgctgttatattttgatatttttgactgaaggtatttcttatcatgtctactctgagtaaactgtgaagttcctgtagttagaatagtaaaccaaccacaagatgtttattttttcataaattgaacgaaaatccacctctcatctgagcgttagcattaataagaataatcacattagcgatggaactgtcaggatagaagcacttgtttatacaaaaccaacgaatttctgcaagttcatgaaaggcttctttaacaactgcagtgagccgccctgtgaatacatatcctgctaatagcattttgtaatctcatacaagccttatgatgcattttcctattgttctgggttggctgaaaagacagcggaggagaatattgtggacagagttattgctgcttttatgctatttttaaacaccttatttgattatgcaaatagcattgcaaaatgaggagaggctacaagaaatgtctcatcttttccactctttaagattatgtttcccacgtgtagtttcccttgttggtgagatagcatttccatgttatctatgttgttttttaactgccttttcacatagtcctagaaagcttgtgacttcatggaggtagcaggaagaaagcagaaagcatagcttaatgcctctttaaatgcattgagcggtgccatggaaagtttgctgagtggatttatgtttcgtaagataaagtagcttacagttatgtaagaataaatgttactcatctctctcctgcccagatgaattatgcttttctataaaaactgttgagttacagcttttaacctggctgtcttgcctttgaaatgtgtaattaggcaaacagtttactgaagtactctacctccatttttcttgcctggaaggtgtgggaagcattctagctgcagaggcacagagctctgcacgcattaatatattctgctcagcagctgactgcagtgtagacacttgcaaatatgaaaacaaagtgaaaaatgtctactctgaagtctgagtgcctgagaagctgttcttttgttgttgttgttgttgtttttgtacttgtttctaagagttcctgcctctcttccctgtgcagataaaacctttctccatctgctccaattttgagtaatcctcttaggttagacctctgctgggagtctggctcctcacatgtggttacctgcttttctgttgtaacctgctcaggaagaagccagctgtagaaaaagggagttgtttcttatgctatgtggttgctagactttcgtgtcaaagtctcccagatacctcttgagcagcaatgcaaagtgtatggaaactcaccaccatttcactgctgatgtgtttgcttaatgtcagtttaattaaagcattggttacttttactatattccaaagggtgaaaatgttttaatcactcttacaggtttgatgctgactaagcctttacttggtaagtgggctactttagcttccaaaaaggaggcttttgtggatttaaaagattaaaaggagtgtttttttctactgtcttcttttgtaaattgctcttctaaagtcttattaaaacatagaattttagaaagtgttttctcagcctaaattggtttaacaatcaccttttaattaaagtcacttgaacgaactttgtcttatccatagtatttgttgcttgtgagtgtggtgtacagttctgtttcactcataggcagtttttttgctctcccttttcccagcctccaagtatgtgacaattacttggaattgtttttcttacccaaatcagaaatatgaagctggaactaaagtgcgtaaggagaaggaaagaacaagtaggtgaactgtatttacttttgtacagactggccagagtacttcttccagaaaggttatgatttggacaatttccaaaaataaaaatctgtttgaagagctgataatgagctgagttttagattttctggctagtggtagagtgtaggatcagttgtcttgaaaccatcactgaaaggtgttcctagctatatagttttgttgtttcaggtatattgttcaactgtacgcttgccaattgcagaactggagttttctttctagcactgagtaacattctcttccatccttgccctgcaagttgacaccattttcatgctagaggcaagcctgatggatcaggggctgccctcagaagggtgcagctgcccatgcagtccttgtctctttctagcagcaggtttggcaatacctgcctggcttagctcagagtgaatttgctaaactcccaggaaactgattttctgctgtgctggagttttgtgccataggccagcagaactacttcattggccatgtgaacaaggtagccagctcagtaagttggcctggtcatgaggacatcaggggatatggcagaaggatgctctctttggcagaggtgtaaacttttacttgactgccttttgaaaacttagcttgaccctgcagaaggtagttgatagttttctactgctgtagctgcctcagctggcacactggtgtgtcggttgtgactggaggtggtgcaagaggtagaacaggacagttctgtgtgtggcagcaagttttaactcggctcagatgtgaaactgcagccacaggaatgtgttaaacatgagatggtgactttccagtgaagtcataggtatttatttctcagccagtgggcataggagcccatggtgtcggcccattctaatggagtgcttttctctaacagcttaatgctgctggtcaagctgagtgttactgagtgcatagagatggtcacatgggaaagaaagagagaattttgtttctgataaatgttcttttaatattagttataagaagttttacatattagatttgtgaaattcagctacgctgttgtaacacttagacacttgcctgtggcttgacttggaagtgcttgtggagagcaatgtgactaacacctcgtgttgcctagtgatgccctttcacttgagctggggtttttttagtgcctgtctggacatgaaagacttagagaaaagctgcaaacaagtgttgactgctagcttgtatctttaattgctttaaaactcgtgggcattctcatgaattatataagcttaagtagttgagaaaatgacataaaattaagtaaatccctgctgaaatcattctcagacagaatttgacaaaaaaaaatcctttcacaagtcttttttgacattttttttctaaaggattttttatggtttcaagactggactgatgcttggggggaaaaaggagttactgaagtggaagcttaactagaaagtttttatttgttgctttgttttctccattatttcgtgaagaattgagagactgtagagccagtttaccaacaaaagtaacctcatgtcttttgagttaggatgaaattttctgggaaagaatggcattcctgcagttattgatagccatggaatcatatatacactgtattcttcatatattgtcaattaaacataaataaaatcctaggaaatggtaaaagcatcaactatcacaccctcttttttctatcttatgactgaattaactttctgtgttttcatgcttttctcctcaaaacacttcataatgtaactggaaaagacacactaatcctagcgtgatgatctgtcagttaccttgtgggttttttcctctttgtctgtcagtgtaaaggtgtatgatagacattctgtacagaacgggctcttagaacaggatttgctgttgagctctacagtaaaccttttattttaattttgcatggatgctcaaggaccactctcattttcatatgtaaaggaaataaacttacgtttttggcaacggcagtaatcagcatctttccttcaggtgtttagtacacttgtacatagtgatcgtgtttgggaagttgtcctgcttggttggctgagggttgtattgtgagatgtgtaacctactatctctgtaagcccagtgctgttgctcgttgtatttaatgccagcagcatcaagttttgtttacaaatccggaatcaggtaactgtatttaaactatgtcagcttgtcatctcccagtcttatttttcagcttaaa	17..1990	4188689	182	48	0	20
+LMAW01000003.1	2833085	2833145	NM_001292086	1000	-	2833085	2833145	0	1	60,	0,	619	679	-	6644	5965,	ggcgcgtgcagcagccatggccgacatggaggagctgttcggcagcgacgccgactcggaggccgagcagaaagataccgattccggctcagactccgactctgaccaggagaacgcgggctccggcagcaacgcctcgggcagcgacagcgagcaggacgacgagcgggaggcagcaaagcccagcaacaaggagctgttcggagacgacagcgaggatgaaggagcctcccatcacacgggcagcgacaaccactccgagaggtcgtacaatcgctccgaagcttcggggcactctgagcacgaagacaacgatcagtcggacgtggaccagcacagcgcttcagaagcggctcatgacgatgaggaggacgagcgggggcacggctctgatgagggcagtcaccattctgagggagatggttcagaaaaggcccattcggaggatgagaagtggggcaaggaggacaaaagcgatcagtcagatgatgaggagcgacagcagaactctgatgatgaggagagacagcagaactcggacgatgaggagaaagcacagaactctgatgaagatgagaggccgcagatgtctgacgatgaggagaggctccagaactcggatgaggagaagatgcagaactctgatgatgaggagaggccgcaggtgtcggacgaggagaagatgcaaaactcagatgatgatgaaagagcccagcactctgatgaggagaagatgcagaactctgacgatgacgaaagggcccagcgctccgatgaggaggagcaggagcataaatctggagagtctgcaagaggcagcgacagtgaagatgaagtcctgcgaatgaagcgaaagaaaccaattgcatcagattcagaggcggacagtgatacagaaggccagaaggaacacgcagacgtcatggacctgtttggaggagcagatgacatttcttcgggaagcgatggggaagacaagccgccaactccaggacagcccattgatgagaatgggctgagccaagaacagcaggaggaagagcctattccagagacaagaatagaggtagaaataccaaaagtaaacacagacttgggtaacgatttgtattttgtgaagctgcccaacttcctcagtgtggagcccagaccatttgatccccagtattatgaggatgaatttgaagatgaggagatgcttgatgaggaagggagaacgagattaaaacttaaggtagaaaacacaatacggtggcggatgcggcgagatgaggaagggaatgagattagagaaagcaatgcccggatagtcaagtggtcggatggaagcatgtctctccacttgggaaatgaggtctttgatgtgtacaaggcaccgctgcagggagatcacacccatctgtttatcagacaagggacaggtctgcaaggacaggctgttttcaggacaaagttaaccttcaggccacactctacagacagtgccacgcacaggaagatgactctgtctctggcagataggtgttcaaagacccagaaaattcgtattttgccaatggcgggtcgtgatccggagtctcagcgcacagaaatgattaagaaagaagaggagagattaagagcttccattcgcagagaatctcagcagcgaagaatgagggagaagcagcatcagcgtggtctgagtgctaattacttagaacccgatcgctatgaagaagaggacgagggagacgatgcgatcagtctagcagctatcaaaaacagatacaaaggtggcatcagagaggaacgtgctagaatctattcttcagacagtgatgaaggctcagatgaagataaaacacaaagactactcaaggcaaagaaacttactagtgatgaggaaggggagccttctggaaagagaaaagcagaggatgatgacaaagcaagtaagaagcataagaagtatgtcatcagtgatgaagaggaagatgatgatgattaacattgagggagcactgaagttgctttctatatatacatatttatatataaattgtacagttctcttacagcaaagatgtaagtagccatattggggttattttgataaaggagaattccattgaaatttgtgtttctggtgtgaataaaagttggtttctttctttttactttctcatatttttacatcttatcttactgcagcagctgctgcaatggggatcatcatagcatcagtttttaaatcttgtacagtacatttcagttttgaaatctatagtacaaactggttgtacaactgaatagaactgaataaatcagtggtcttactgagttcattaggagaaatcataatcttcatatagaatgcttaaattataagttttctcagccaggttatggagatgaaggttaccatttgtacagaagatttggaatatcatatgagtggcacaacaccgtactgttttttcctgcactttcctattacgtactgctggctgtagatggtacattactgtgctgttatattttgatatttttgactgaaggtatttcttatcatgtctactctgagtaaactgtgaagttcctgtagttagaatagtaaaccaaccacaagatgtttattttttcataaattgaacgaaaatccacctctcatctgagcgttagcattaataagaataatcacattagcgatggaactgtcaggatagaagcacttgtttatacaaaaccaacgaatttctgcaagttcatgaaaggcttctttaacaactgcagtgagccgccctgtgaatacatatcctgctaatagcattttgtaatctcatacaagccttatgatgcattttcctattgttctgggttggctgaaaagacagcggaggagaatattgtggacagagttattgctgcttttatgctatttttaaacaccttatttgattatgcaaatagcattgcaaaatgaggagaggctacaagaaatgtctcatcttttccactctttaagattatgtttcccacgtgtagtttcccttgttggtgagatagcatttccatgttatctatgttgttttttaactgccttttcacatagtcctagaaagcttgtgacttcatggaggtagcaggaagaaagcagaaagcatagcttaatgcctctttaaatgcattgagcggtgccatggaaagtttgctgagtggatttatgtttcgtaagataaagtagcttacagttatgtaagaataaatgttactcatctctctcctgcccagatgaattatgcttttctataaaaactgttgagttacagcttttaacctggctgtcttgcctttgaaatgtgtaattaggcaaacagtttactgaagtactctacctccatttttcttgcctggaaggtgtgggaagcattctagctgcagaggcacagagctctgcacgcattaatatattctgctcagcagctgactgcagtgtagacacttgcaaatatgaaaacaaagtgaaaaatgtctactctgaagtctgagtgcctgagaagctgttcttttgttgttgttgttgttgtttttgtacttgtttctaagagttcctgcctctcttccctgtgcagataaaacctttctccatctgctccaattttgagtaatcctcttaggttagacctctgctgggagtctggctcctcacatgtggttacctgcttttctgttgtaacctgctcaggaagaagccagctgtagaaaaagggagttgtttcttatgctatgtggttgctagactttcgtgtcaaagtctcccagatacctcttgagcagcaatgcaaagtgtatggaaactcaccaccatttcactgctgatgtgtttgcttaatgtcagtttaattaaagcattggttacttttactatattccaaagggtgaaaatgttttaatcactcttacaggtttgatgctgactaagcctttacttggtaagtgggctactttagcttccaaaaaggaggcttttgtggatttaaaagattaaaaggagtgtttttttctactgtcttcttttgtaaattgctcttctaaagtcttattaaaacatagaattttagaaagtgttttctcagcctaaattggtttaacaatcaccttttaattaaagtcacttgaacgaactttgtcttatccatagtatttgttgcttgtgagtgtggtgtacagttctgtttcactcataggcagtttttttgctctcccttttcccagcctccaagtatgtgacaattacttggaattgtttttcttacccaaatcagaaatatgaagctggaactaaagtgcgtaaggagaaggaaagaacaagtaggtgaactgtatttacttttgtacagactggccagagtacttcttccagaaaggttatgatttggacaatttccaaaaataaaaatctgtttgaagagctgataatgagctgagttttagattttctggctagtggtagagtgtaggatcagttgtcttgaaaccatcactgaaaggtgttcctagctatatagttttgttgtttcaggtatattgttcaactgtacgcttgccaattgcagaactggagttttctttctagcactgagtaacattctcttccatccttgccctgcaagttgacaccattttcatgctagaggcaagcctgatggatcaggggctgccctcagaagggtgcagctgcccatgcagtccttgtctctttctagcagcaggtttggcaatacctgcctggcttagctcagagtgaatttgctaaactcccaggaaactgattttctgctgtgctggagttttgtgccataggccagcagaactacttcattggccatgtgaacaaggtagccagctcagtaagttggcctggtcatgaggacatcaggggatatggcagaaggatgctctctttggcagaggtgtaaacttttacttgactgccttttgaaaacttagcttgaccctgcagaaggtagttgatagttttctactgctgtagctgcctcagctggcacactggtgtgtcggttgtgactggaggtggtgcaagaggtagaacaggacagttctgtgtgtggcagcaagttttaactcggctcagatgtgaaactgcagccacaggaatgtgttaaacatgagatggtgactttccagtgaagtcataggtatttatttctcagccagtgggcataggagcccatggtgtcggcccattctaatggagtgcttttctctaacagcttaatgctgctggtcaagctgagtgttactgagtgcatagagatggtcacatgggaaagaaagagagaattttgtttctgataaatgttcttttaatattagttataagaagttttacatattagatttgtgaaattcagctacgctgttgtaacacttagacacttgcctgtggcttgacttggaagtgcttgtggagagcaatgtgactaacacctcgtgttgcctagtgatgccctttcacttgagctggggtttttttagtgcctgtctggacatgaaagacttagagaaaagctgcaaacaagtgttgactgctagcttgtatctttaattgctttaaaactcgtgggcattctcatgaattatataagcttaagtagttgagaaaatgacataaaattaagtaaatccctgctgaaatcattctcagacagaatttgacaaaaaaaaatcctttcacaagtcttttttgacattttttttctaaaggattttttatggtttcaagactggactgatgcttggggggaaaaaggagttactgaagtggaagcttaactagaaagtttttatttgttgctttgttttctccattatttcgtgaagaattgagagactgtagagccagtttaccaacaaaagtaacctcatgtcttttgagttaggatgaaattttctgggaaagaatggcattcctgcagttattgatagccatggaatcatatatacactgtattcttcatatattgtcaattaaacataaataaaatcctaggaaatggtaaaagcatcaactatcacaccctcttttttctatcttatgactgaattaactttctgtgttttcatgcttttctcctcaaaacacttcataatgtaactggaaaagacacactaatcctagcgtgatgatctgtcagttaccttgtgggttttttcctctttgtctgtcagtgtaaaggtgtatgatagacattctgtacagaacgggctcttagaacaggatttgctgttgagctctacagtaaaccttttattttaattttgcatggatgctcaaggaccactctcattttcatatgtaaaggaaataaacttacgtttttggcaacggcagtaatcagcatctttccttcaggtgtttagtacacttgtacatagtgatcgtgtttgggaagttgtcctgcttggttggctgagggttgtattgtgagatgtgtaacctactatctctgtaagcccagtgctgttgctcgttgtatttaatgccagcagcatcaagttttgtttacaaatccggaatcaggtaactgtatttaaactatgtcagcttgtcatctcccagtcttatttttcagcttaaa	17..1990	4188689	49	11	0	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_cds.bigpsl	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,12 @@
+LMAW01000001.1	517465	615765	NM_001012804	1000	-	517465	615765	0	18	139,137,107,81,142,58,94,3,171,39,114,150,87,2,112,74,32,119,	0,5531,10924,11277,14625,16705,17663,21512,21597,27451,32690,33190,43784,44910,44925,57174,98049,98181,	121	2062	-	4592	2530,2669,2806,2914,2995,3137,3195,3289,3292,3487,3721,3844,4036,4123,4125,4246,4320,4352,		68..2092	10443977	1247	370	0	44
+LMAW01000001.1	9729332	9765132	NM_204766	1000	+	9729332	9765132	0	8	108,153,66,93,39,171,99,84,	0,4809,21687,25888,32710,33223,35333,35716,	262	2188	+	5992	262,388,574,688,1414,1459,1981,2104,		50..5863	10443977	537	234	0	42
+LMAW01000001.1	10027590	10064141	NM_001006176	1000	+	10027640	10063890	0	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,	0,3564,3763,3927,5671,6106,6864,8056,15894,16204,32078,32234,32383,33208,33389,33675,33897,34150,34357,34553,34775,34994,35153,35411,35598,35793,36026,36216,36524,	296	3230	+	3248	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,		347..3118	10443977	2134	377	0	62
+LMAW01000002.1	103604	131424	NM_204766	1000	+	103604	131424	0	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,	0,803,4160,4305,4398,4629,4653,5657,8443,9363,9432,9544,10653,10787,11262,12579,12834,12989,13304,14163,14426,15078,16515,17068,17725,18581,19120,19914,20341,20845,21300,22189,22294,23186,23801,23939,24113,24451,25634,25838,26157,26416,26650,27499,27733,	49	5815	+	5992	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,		50..5863	5883884	3724	1107	0	326
+LMAW01000002.1	3610886	3618513	NM_001031013	1000	+	3610955	3618513	0	5	33,66,21,276,138,	0,69,7055,7213,7489,	69	702	+	971	69,138,232,285,564,		121..822	5883884	420	114	0	0
+LMAW01000003.1	259524	268833	NM_204766	1000	+	259524	268833	0	5	27,80,11,66,36,	0,1731,2005,2855,9273,	574	1453	+	5992	574,700,780,847,1417,		50..5863	4188689	143	58	0	19
+LMAW01000003.1	2559457	2573393	NM_204766	1000	+	2559457	2573393	0	5	84,66,33,13,66,	0,3787,3892,11310,13870,	553	1588	+	5992	553,739,844,1457,1522,		50..5863	4188689	189	73	0	0
+LMAW01000003.1	2820233	2835138	NM_001292086	1000	-	2823535	2835132	0	37	27,162,54,12,11,18,45,15,93,29,26,161,23,21,106,70,125,72,9,34,23,90,69,90,72,93,171,137,135,93,87,146,90,5,107,727,64,	0,100,289,415,466,601,625,753,805,1069,1098,1190,1352,1546,1601,1712,1782,1910,2192,2202,2337,2841,3036,3121,3302,6920,7314,7796,8505,8919,9349,10865,11395,11653,12233,12598,14841,	10	5375	-	6644	1269,1369,1559,1691,1751,1884,1911,2026,2075,2352,2382,2475,2636,2829,2891,2998,3074,3206,3565,3574,3703,4204,4412,4505,4687,4759,4856,5043,5180,5315,5408,5495,5641,5731,5736,5843,6570,		17..1990	4188689	2710	404	0	198
+LMAW01000003.1	2832850	2833124	NM_001292086	1000	-	2832850	2833124	0	2	140,110,	0,164,	481	731	-	6644	5913,6053,		17..1990	4188689	200	50	0	0
+LMAW01000003.1	2832851	2833151	NM_001292086	1000	-	2832851	2833151	0	2	74,43,	0,257,	562	679	-	6644	5965,6039,		17..1990	4188689	92	25	0	0
+LMAW01000003.1	2832901	2833151	NM_001292086	1000	-	2832901	2833151	0	2	148,102,	0,148,	508	782	-	6644	5862,6034,		17..1990	4188689	182	48	0	20
+LMAW01000003.1	2833085	2833145	NM_001292086	1000	-	2833085	2833145	0	1	60,	0,	619	679	-	6644	5965,		17..1990	4188689	49	11	0	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_fa.bigpsl	Wed Apr 12 17:38:51 2017 -0400
@@ -0,0 +1,12 @@
+LMAW01000001.1	517465	615765	NM_001012804	1000	-	517465	615765	0	18	139,137,107,81,142,58,94,3,171,39,114,150,87,2,112,74,32,119,	0,5531,10924,11277,14625,16705,17663,21512,21597,27451,32690,33190,43784,44910,44925,57174,98049,98181,	121	2062	-	4592	2530,2669,2806,2914,2995,3137,3195,3289,3292,3487,3721,3844,4036,4123,4125,4246,4320,4352,	ggttcggcggccgccggacggttgcgtgacgaggcgggcagatccttctggatacgagcggagagccatggccgacgtgttcccgggctccgagcccggcgcggccccggacgcggcgcggcgctttgctcgcaaaggggccctgaggcagaagaacgtgcacgaggtgaaggagcacaaattcatcgcgcgcttcttcaagcagcccaccttctgcagccactgcaccgacttcatctggggatttgggaaacaaggatttcagtgccaagtttgctgttttgtggttcataagagatgccatgagttcgttaccttctcctgtcctggagctgacaagggacctgacaccgatgaccccaggagcaagcacaaatttaagatccacacctatgggagcccaaccttctgtgaccactgtgggtcccttctttatgggctcctacaccaagggatgaaatgtgacacttgtgatatgaatgtgcataagcaatgtgtgataaacgtcccgagcctctgtggcatggatcacactgagaaaaggggaaggatttatctgaaggctgaagtcactggtgacaaactggaagtaacagtgcgagaagcaaaaaacctaattcccatggatccaaatgggctttcagatccttatgttaaactgaaacttatcccagatcccaagaatgaaagtaaacaaaaaacaaaaaccttccgttctaccctgaatccacactggaatgagtcattcacatttaaattaaaacctacagacaaagatcgacggctctctgtagaggtctgggactgggatcgaacaaccaggaatgattttatgggctctctttcatttggggtgtcagagctcatgaagatgccagccagtggatggtacaagctgctgaatcaagaagaaggtgaatattataatgttccaattccagatgctgacgaggatggaaatgcagagctccggcagaagttcgagaaagccaaacttgggccagctggtaacaaagtcattactccatcagaagacaggaattcaagtgtgccatccaacaatctggacagggtgaaactgacagatttcaactttcttatggttcttggaaaaggaagctttggaaaggtgatgctggcggacaggaagaatacagaggagctctatgcaatcaaaatactgaaaaaagatgtggtgattcaggatgatgatgttgagtgtacaatggttgaaaaacgagtgctagcactgcaggataaaccaccattcctgacacagcttcactcatgtttccaaacagttgaccgcctgtattttgttatggagtatgtgaatggtggggatctcatgtaccacattcagcaagtaggaaaatttaaggagccacaagcagtgttctatgcagctgagatctcagttgggttattctttctccataatagagggattgtttatagagatctgaaattggataatgtgatgttggattcagaaggacacattaaaattgctgactttggaatgtgcaaagaacatatgttagatggagtaacaaccaggaccttctgtggcaccccagattacatcgcaccggagatcattgcttatcagccctatgggaagtctgtggattggtgggcatatggagtgctgctctacgagatgttagctggccagcctccatttgatggagaagatgaagatgaacttttccagtccataatggaacataatgtttcctatccaaaatcgctgtccaaagaagctgtctccatctgcaaggggctaatgactaaacatcccgcaaagcgccttggctgcggcctcgaaggtgaaagagacatcagggaacacgctttcttcaggagaattgactgggagaaactggaaaacagagagatccagccacctttcaagcccaaagtgtgtggcaaaggtgctgaaaacttcgataaattcttcacgcgaggacagccggtgttgaccccgccagaccagctggtcattgctaacatagatcaatccgattttgaagggttctcctatgtcaacccccagtttgtacatcccctcctagaaaatgtagcatgaaacagcagaacaggaacaaatcccgcagtggggaacggttcttaaccctaaaatttttaggtttttgccttgattccgtttgggcctgaaaattatagggttagaaagtgtaagatgggagaaaggccacttagtgaggattttgactttgcaaccaaaacgtcttaatgggagataaattagcatacagtgcccatttctcctactagaagtcaccatgactcgtctgaagttccccatttttggtacattctgtagttctgtagctccccgctgtccttttgctccgtttttcactccgctgctgttacaaataatccaagacccgacctgagaagcacctccagtactcagtccttgcaggggaccagctccccgctcctatgggcaccatggggagagcagcgcacgggactggagagcgccggggaggagaggcattgcagaatgtggtggaaagcagttgttaccaaaacccgacaaataaatacgagttgggagtgggagggcaggggggatgaaatcctattagagcccaaagcttcgtgaaccaatcctgtaagcaacaccaaatttaaacacgctccggcagtggccagatctctagatctttgctaagtagcatgtgataaactcgagggtgaagttttgtctttaataataataataatagtaataattttaataatatttttgtgaattttaatctccgtgagattattctgtgatccagggtgccattgtttgttcagttgatttcatttgcaccactcctcaagctcactgttgactggttctaataacaccaacgttttactatgagatttgttaacctggaatgtaaaacagaactgtaatcccttacatcttatttacttgtgtgtgttgtagtctgcagtatagggcagtaaattgaaggaagtattgtgtatgctaaattaacaaaaacgcagtcccaggtgactccctgatttttccagaacaactcatgaaaatgaattgagatttagttctacagtaatcaattctaactcagaaaacttggggctgtacaataaccaagcttgaaagaagcacctgaagcttgttttattggcagaatggaatttaacacattttacatacgcttcatgcaatgaattttgcatgtttagtaataactcttaataataagagttaataataagcagttctatattgacattaccatatcaagcatacagagtattacaaaagttttataaaacaaattgtgctttatttgtggaagtacttgttctgaacgacatcatttaggtttagctcaatgttttcttgctgttgttttgggttgtttttttctagtttttggatattgttaatgacttagggtatcatctgtttttttaaacgtagatctacttttaaacaataattgctacctgcaggttttatacaagtttcaattaggcttttgtttcatgtctgctgattactgacagggaaagaaatagattttatttgcaatgatgaacgctgtaattaatgcaatcttctcctctcctatctcacttagatacaaattttgatatttcctcttaccaacttaccagaagatcttaattcaaatatcagtaaatatttttgtgcttactttggttttgttacagcatgtaaaatagtaggcggtgcgttttccttttcttcccttcagcctcgttaatggtagcagccataggcactctttgtctgtcggatgtgcatgatgatgccagaagcatgatgtctctgttgctgcatgcagactgaatacagtttttccagcatgtaaacatattcaaaaagtcagatatttgccataaaagacttacatttatactagaatatgtaaccggagggtgggggtgggagcggggggggaggaatctactttctaatcatcttttattacaataaaacattgagcctgtgccaaagattctgctagaaagatccagtcctgcagattggacggcgatgatgtgcaggagtgaccccgtggcacatgggacagttggtgagcgaaccgcagctggatgtgagcagaagcggccgtgcggtgctcctgcaccacggatgccttccaaagccgtcctttggcgcctgggatttgcagcactccagttgtgtgaccagccctgcttcctttgtggtcacagccctaaggttggagcatccccagagagggctcagcccgtgttggatggacccggcgctgacacatggcatcccccaacgaacagctccccagattgttgcctaaataaacagaactcaaacattttaatacattttaggagtacagtttttcaactatccggtgtcagatatgttatcagccaaatttgggcattcgttttcctctttgtgtattatatacctgaagattatggtatgttgttccccataaagcatgtggactagtgcagcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaa		10443977	1247	370	0	44
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