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Changeset 1:96d135d3c57f (2015-06-03)

Previous changeset 0:d6abffbc9ee7 (2015-05-21) Next changeset 2:affc5ec4f65a (2015-07-31)

Commit message:
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty

modified:
flaimapper-gtf-from-fasta.xml
flaimapper.xml
tool_dependencies.xml

added:
test-data/test1/ncrnadb09.fa
test-data/test1/ncrnadb09.v2.gtf
test-data/test1/snord81.bam
test-data/test1/snord81.flaimapper.txt
test-data/test2/test_genomic_SE_reads.fastqsanger
test-data/test2/test_genomic_alignment.bam
test-data/test2/test_genomic_all_chromosomes.fa
test-data/test2/test_genomic_flaimapper_output.txt
test-data/test2/test_genomic_genes.gtf
test-data/test3/ncrnadb09.fa
test-data/test3/reference.gtf

removed:
egg/flaimapper-1.1.5-py2.7.egg
test-data/ncrnadb09.fa
test-data/ncrnadb09.fa.fai
test-data/ncrnadb09.gtf
test-data/snord81.bam
test-data/snord81.flaimapper.txt

diff -r d6abffbc9ee7 -r 96d135d3c57f egg/flaimapper-1.1.5-py2.7.egg

Binary file egg/flaimapper-1.1.5-py2.7.egg has changed

diff -r d6abffbc9ee7 -r 96d135d3c57f flaimapper-gtf-from-fasta.xml
--- a/flaimapper-gtf-from-fasta.xml Thu May 21 07:26:46 2015 -0400
+++ b/flaimapper-gtf-from-fasta.xml Wed Jun 03 07:57:12 2015 -0400

@@ -1,9 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.1.5.b">
+<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1">
<description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
<requirements>
- <requirement type="package" version="0.8.2.1">pysam</requirement>
- <requirement type="package" version="1.1.5">flaimapper</requirement>
+ <requirement type="package" version="1.2.1">flaimapper</requirement>
</requirements>

<stdio>
@@ -32,9 +31,9 @@

<tests>
<test>
- <param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
+ <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />

- <output name="output" file="ncrnadb09.gtf" />
+ <output name="output" file="test3/reference.gtf" />
</test>
</tests>

diff -r d6abffbc9ee7 -r 96d135d3c57f flaimapper.xml
--- a/flaimapper.xml Thu May 21 07:26:46 2015 -0400
+++ b/flaimapper.xml Wed Jun 03 07:57:12 2015 -0400

[

@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a">
+<tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1">
<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
<requirements>
- <requirement type="package" version="0.8.2.1">pysam</requirement>
- <requirement type="package" version="1.1.5">flaimapper</requirement>
+ <requirement type="package" version="1.2.1">flaimapper</requirement>
</requirements>

<stdio>
+ <regex match="in parse_gff.*?ValueError: invalid literal for int with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" />
<regex match="[fai_load] build FASTA index." source="stderr" level="log" />
</stdio>

@@ -45,13 +45,21 @@
</outputs>

<tests>
- <test>
- <param name="alignments" value="snord81.bam" ftype="bam" />
- <param name="mask" value="ncrnadb09.gtf" ftype="gtf" />
- <param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
- <param name="output_format" value="1" />
+ <test>
+ <param name="alignments" value="test1/snord81.bam" ftype="bam" />
+ <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" />
+ <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" />
+ <param name="output_format" value="1" />

- <output name="output" file="snord81.flaimapper.txt" />
+ <output name="output" file="test1/snord81.flaimapper.txt" />
+ </test>
+ <test>
+ <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" />
+ <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" />
+ <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" />
+ <param name="output_format" value="1" />
+
+ <output name="output" file="test2/test_genomic_flaimapper_output.txt" />
</test>
</tests>

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/ncrnadb09.fa
--- a/test-data/ncrnadb09.fa Thu May 21 07:26:46 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,4538 +0,0 @@\n->HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\n-GCGCTGCCCCGTGAGCAGTCTCCACCACCTCCCCTGCAAACGTCCAGTGGTGCAGAGGTAATGGACGTTGGCTCTGGTGGTGATGGACAGTCCGAACTCCCTGCT\n->HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\n-TTGATGCTAGACAGGTAGTGTCCCTCAGGGCTGTAGAACAGGGCTGGGATTACTAAAGCCCTGTTCTATGCCCTGAGGGACACTGAGCATGTCATTTCACTTCT\n->HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\n-ATGGTGGGCTGCCACCAAGAAGGTGAAGGGAGGGTCAGTCCCAATCTGAATCCCACCAAAATAGGTGGTAGAGGGTTGCCCTCCTTTCTTCCCTCACCTCTGACCCCGCTCTTCG\n->HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\n-TGCCACCTCATGGTACTCGGAGGGAGGTTGTCCGTGGTGAGTTCGCATTATTTAATGATGCCCAATACACGGTCGACCTCTTTTCGGTATCAGATCTCACCA\n->HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\n-AACCCCAATATGCCAATGCCTATCACATATCTGCCTGTCCTATGACAAACATGGCAGGTAGATATTTGATAGGCATTGGCACACTGGCAAA\n->HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\n-CTGGCCTAAAATATATGAAATGTAGAGATTGATCAAAATAGTTTCTATCAAAATAGTTTTGATCAATCTCTGCAATTTTATATATGAGGAAACTG\n->HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\n-TTTTTGCTGATTTTTTTTTAGTATTTTTCCATCAGTGTTCATAAGGAATGTTGCTCTGTAGTTTTCTTATAGTGTGGCTTTCTTAGAGCAAAGATGGTTCCCTATTACTTTCTA\n->HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\n-AAATGGGCTTTCAGAAGAAAAAACAGGAGATAAAGTTTGTGATAATGTTTGTCTATATAGTTATGAATGTTTTTTCCTGTTTCCTTCAGGGCCATAATACTCCC\n->HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\n-GTCCTGGGTTGGGTCGATGATGAGAACCTTATATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\n-CCATCACTTGCCCCAGCTAGGTAAAGAGCCCTGTGGAGACACCTGGATTCAGAGAACATGTCTCCACTGAGCACTTGGGCCTTGATGGCGGCTCTTGTTCCAA\n->HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\n-TGTGTCGGGGGTCCAGGCAGGAGCCGGACTGGACCTCAGGGAAGAGGCTGACCCGGCCCCTCTTGCGGCAGGCTTCACC\n->HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\n-AAAATTGAATAGTGAGCAACCCAGTGGGCTATGGAAATGTGTGGAAGATGGCATTTCTATTTCTCAGTGGGGCTCTTACCTATTACTCAT\n->HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\n-TATGTCAAGTATAGCCAATCATTAGTATTCTGAGCTGTAGGAATCAAAGATTTTGATTAGATTCTGTAACTCAGAGGTTTATTAGAAAAAA\n->HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\n-CCGCTCCAGCCCTGCCGGGGCTAAAGTGCTGACAGTGCAGATAGTGGTCCTCTCCGTGCTACCGCACTGTGGGTACTTGCTGCTCCAGCAGGGCACGCACAG\n->HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\n-GTCCTAGGTTGGGTCAATGATGAGAACCTTATAATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n->HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]'..b'ME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGCGGTtATCACGTCTGCTTTACACGCAGAAGGtCCTGGGTTCGAGCCCCAGTGGAACCAcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGCtAGCGCGTTTGGCTGTTAACTAAAAAGtTGGTGGTTCGAACACACCCAGAGGCGcca\n->NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\n-GTCTCTGTGGCGCAATCGGTtAGCGCATTCGGCTGTTAACCGAAAGGtTGGTGGTTCGAGCCCACCCAGGGACGcca\n->NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\n-GGCAGTAAAGTAGGGTGGTtAAGACAAGGGGCTCTGGAGCAAGACTGCCCAAGATCAAATCCTGGTGCTGCCAcca\n->NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\n-CCTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGATCCTTAGGtCGCTGGTTCGATTCCGGCTCGAAGGAcca\n->NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\n-GGTTCCATAGTGTAGTGGTtATCACATCTGCTTTACACGCAGAAGGtCCTGGGTTCAAGCCCCAGTGGAACCAcca\n->NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\n-GCAGCGATGGCCGAGTGGTtAAGGCGTTGGACTTGAAATCCAATGGGGTCTCCCCGCGCAGGTTCGAACCCTGCTCGCTGCGcca\n->NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\n-GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCATGGGTTTGAGCCCCACGTTTGGTGcca\n->NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\n-GGCAGAATGGTGCAGCGGTtcAGCACCCAGGCTCTGCAGCCAGCTGTTGCCTGGGCTCAAATCCCAGCTCTGCCAcca\n->HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene 1&LOCI=[chr22:42471953-42472275:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008259&GENOME=hg19\n-ATTGTTGAACTATAGGGTATGAACTATAGGGTGTCCAGTGTACAGCATTTTATGGCTACTTGGTGTCACTCTAGAGCCACATAGCAAGTGGCTTCAAGAGGTAATTCTTGATCCTTTTGTAGTTCATGAGCGTGATGATTGGGTGTTCACATGCATGTGTGAGCTGTGCCACCCTCGAACCTTGTTACCATGTAGGCACATTACCGATCTGACATGAAGAAAAGAAAAGAAAAAAAAAGAAAAAGAGATAATTCTTTAGCTCAAGGGAGGAGTAAGACTTGACAGCTGTTGCGTTTCAGTATGTCTGGGCCTGATTATTTAAA\n->HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\n-ATACGTGGCTGGGTTGCCATGCTCCATCTGCTGAGAGGCGTATTGTGAGTGGCAGGTGTTATGGATCACAGCCTCTGCATATGTGCCAGCAGAAAAAGTAATTGTAACCAGCAAAGCATTTTACTACATAAACGTTTTAGCCCCTATAAAAACATCCGGAGATCCTTTTGTTGTTCATGAGCATGACAATTGGGTGTTTTCATGCAGCGAGTGAGATGTGCCACCCTGGAACCTTGTTACGACGTCGCATGTTACCTGTCTGACCTGAAAAATAATTAATAAGTAAAACATACGGAAGCCAGTTTCTCATGGCTATTTCCAACTAGTCACTTGAAGAATATGGAATTAGTTATACAATTAGTTATACGTTGTATAACCATCATAAAATTAGTTACAGATTGATGTGACATTATCTTGAAATTAAT\n->HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\n-GAGGGTTCTCAGCTTGAAGTTCCTTGTGCCTCTTTTAGGGAAGACACTCAGATGGTATATCGAGTATAAAATGACTTAGCGATTCTTCTCCTCAAAATGTGTCATTTATGATCCTTTTGTAGTTCATGAGTGTGATGATTGTGTGTTCATACGCTTGTGTGAGATGTGCCACCCTTGAACCTTGTTACGACATTGGCACATTACCCGTCTGATCTGAAAAAAAAAGTATCATTTATTTACTTACCTAAAATCTATGGAGTGCTTACTATGTGCCAAGTGCTTTTTAAAGCACTTGGAATACCTGACTGCATGAACAGAAACA\n->HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\n-TGTATGTGGGAATGAATGATGACAAAATGTTTCAGTCCCAAATGATACATACTGATTATACCATTATATTTATCCTGACATTCCTCTAAGGCTTT\n->HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\n-TGCCTCTAGGGGCTGGCTTTAGCTCAGCGGTTACTTCGACAATGCTTTCCATGGTTAGGAAACCAACCTCTCTGGGTGGTTTGAGACCCGTGGGCCCTCTCCAGTCCTTTTGTGGTCGCCA\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/ncrnadb09.fa.fai
--- a/test-data/ncrnadb09.fa.fai Thu May 21 07:26:46 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2269 +0,0 @@\n-HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\t105\t149\t105\t106\n-HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\t104\t404\t104\t105\n-HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\t115\t657\t115\t116\n-HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\t102\t924\t102\t103\n-HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\t91\t1177\t91\t92\n-HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\t95\t1419\t95\t96\n-HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\t114\t1662\t114\t115\n-HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\t104\t1926\t104\t105\n-HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\t101\t2208\t101\t102\n-HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\t103\t2459\t103\t104\n-HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\t79\t2713\t79\t80\n-HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\t90\t2944\t90\t91\n-HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\t91\t3212\t91\t92\n-HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\t102\t3452\t102\t103\n-HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\t102\t3732\t102\t103\n-HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\t91\t4003\t91\t92\n-HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\t105\t4345\t105\t106\n-HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\t152\t4620\t152\t153\n-HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\t152\t4941\t152\t153\n-HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\t122\t5243\t122\t123\n-HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\t102\t5515\t102\t103\n-HGNC=33680&HUGO-Symbol=MIR937&HUGO-Name=microRNA_937&LOCI=[chr8:144895117-144895222:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030633&GENOME=hg19\t106\t5766\t106\t107\n-HGNC=38339&HUGO-Symbol=MIR4273&HUGO-Name=microRNA_4273&LOCI=[chr3:75787421-75787524:strand=+]&SOURCE=Ref'..b'=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr16.tRNA10-LysCTT&GENOME=hg19\t76\t573624\t76\t77\n-NAME=TRNAGlnTTG&LOCI=[chr16:3419813-3419884:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr16.tRNA14-GlnTTG&GENOME=hg19\t75\t573817\t75\t76\n-NAME=TRNAGluCTC&LOCI=[chr1:249168447-249168518:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA59-GluCTC&GENOME=hg19\t75\t574011\t75\t76\n-NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\t76\t574235\t76\t77\n-NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\t75\t574430\t75\t76\n-NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\t75\t574624\t75\t76\n-NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\t77\t574818\t77\t78\n-NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\t78\t575013\t78\t79\n-NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\t77\t575209\t77\t78\n-NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\t75\t575402\t75\t76\n-NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\t77\t575631\t77\t78\n-NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\t76\t575827\t76\t77\n-NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\t74\t576022\t74\t75\n-NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\t85\t576214\t85\t86\n-NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\t76\t576418\t76\t77\n-NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\t77\t576613\t77\t78\n-NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\t77\t576844\t77\t78\n-NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\t76\t577044\t76\t77\n-NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\t76\t577236\t76\t77\n-NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\t76\t577428\t76\t77\n-NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\t85\t577622\t85\t86\n-NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\t76\t577825\t76\t77\n-NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\t78\t578024\t78\t79\n-HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\t323\t578285\t323\t324\n-HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\t425\t578788\t425\t426\n-HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\t322\t579395\t322\t323\n-HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\t95\t579895\t95\t96\n-HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\t121\t580153\t121\t122\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/ncrnadb09.gtf
--- a/test-data/ncrnadb09.gtf Thu May 21 07:26:46 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,2269 +0,0 @@\n-HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t0\t105\t1\t+\t0\n-HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t0\t104\t1\t-\t0\n-HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t0\t115\t1\t-\t0\n-HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t+\t0\n-HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t-\t0\n-HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t0\t95\t1\t+\t0\n-HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t0\t114\t1\t+\t0\n-HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t0\t104\t1\t+\t0\n-HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t0\t101\t1\t+\t0\n-HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t0\t103\t1\t-\t0\n-HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t0\t79\t1\t-\t0\n-HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t0\t90\t1\t-\t0\n-HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t+\t0\n-HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t-\t0\n-HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t+\t0\n-HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t+\t0\n-HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t0\t105\t1\t-\t0\n-HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t0\t152\t1\t-\t0\n-HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t0\t152\t1\t-\t0\n-HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t0\t122\t1\t-\t0\n-HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t-\t0\n-H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t+\t0\n-NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n-NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t+\t0\n-NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t-\t0\n-NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n-NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t0\t78\t1\t-\t0\n-NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n-NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t-\t0\n-NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n-NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n-NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t0\t74\t1\t+\t0\n-NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t0\t85\t1\t-\t0\n-NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n-NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n-NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n-NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t+\t0\n-NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t+\t0\n-NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n-NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t0\t85\t1\t+\t0\n-NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n-NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t0\t78\t1\t-\t0\n-HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t0\t323\t1\t-\t0\n-HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t0\t425\t1\t+\t0\n-HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t0\t322\t1\t-\t0\n-HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t0\t95\t1\t+\t0\n-HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t0\t121\t1\t+\t0\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/snord81.bam

Binary file test-data/snord81.bam has changed

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/snord81.flaimapper.txt
--- a/test-data/snord81.flaimapper.txt Thu May 21 07:26:46 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,4 +0,0 @@
-Fragment Precursor 5' 3' Sequence Corresponding-reads
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_1 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 37 ATACATGATGATCTCAATCCAAC 99
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_2 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 68 CTCACTGATTACTTGATGACAA 171
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_3 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 80 TTACTTGATGACAATAAAATATCTGA 82

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test1/ncrnadb09.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1/ncrnadb09.fa Wed Jun 03 07:57:12 2015 -0400

[

b'@@ -0,0 +1,4538 @@\n+>HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\n+GCGCTGCCCCGTGAGCAGTCTCCACCACCTCCCCTGCAAACGTCCAGTGGTGCAGAGGTAATGGACGTTGGCTCTGGTGGTGATGGACAGTCCGAACTCCCTGCT\n+>HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\n+TTGATGCTAGACAGGTAGTGTCCCTCAGGGCTGTAGAACAGGGCTGGGATTACTAAAGCCCTGTTCTATGCCCTGAGGGACACTGAGCATGTCATTTCACTTCT\n+>HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\n+ATGGTGGGCTGCCACCAAGAAGGTGAAGGGAGGGTCAGTCCCAATCTGAATCCCACCAAAATAGGTGGTAGAGGGTTGCCCTCCTTTCTTCCCTCACCTCTGACCCCGCTCTTCG\n+>HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\n+TGCCACCTCATGGTACTCGGAGGGAGGTTGTCCGTGGTGAGTTCGCATTATTTAATGATGCCCAATACACGGTCGACCTCTTTTCGGTATCAGATCTCACCA\n+>HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\n+AACCCCAATATGCCAATGCCTATCACATATCTGCCTGTCCTATGACAAACATGGCAGGTAGATATTTGATAGGCATTGGCACACTGGCAAA\n+>HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\n+CTGGCCTAAAATATATGAAATGTAGAGATTGATCAAAATAGTTTCTATCAAAATAGTTTTGATCAATCTCTGCAATTTTATATATGAGGAAACTG\n+>HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\n+TTTTTGCTGATTTTTTTTTAGTATTTTTCCATCAGTGTTCATAAGGAATGTTGCTCTGTAGTTTTCTTATAGTGTGGCTTTCTTAGAGCAAAGATGGTTCCCTATTACTTTCTA\n+>HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\n+AAATGGGCTTTCAGAAGAAAAAACAGGAGATAAAGTTTGTGATAATGTTTGTCTATATAGTTATGAATGTTTTTTCCTGTTTCCTTCAGGGCCATAATACTCCC\n+>HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\n+GTCCTGGGTTGGGTCGATGATGAGAACCTTATATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n+>HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\n+CCATCACTTGCCCCAGCTAGGTAAAGAGCCCTGTGGAGACACCTGGATTCAGAGAACATGTCTCCACTGAGCACTTGGGCCTTGATGGCGGCTCTTGTTCCAA\n+>HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\n+TGTGTCGGGGGTCCAGGCAGGAGCCGGACTGGACCTCAGGGAAGAGGCTGACCCGGCCCCTCTTGCGGCAGGCTTCACC\n+>HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\n+AAAATTGAATAGTGAGCAACCCAGTGGGCTATGGAAATGTGTGGAAGATGGCATTTCTATTTCTCAGTGGGGCTCTTACCTATTACTCAT\n+>HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\n+TATGTCAAGTATAGCCAATCATTAGTATTCTGAGCTGTAGGAATCAAAGATTTTGATTAGATTCTGTAACTCAGAGGTTTATTAGAAAAAA\n+>HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\n+CCGCTCCAGCCCTGCCGGGGCTAAAGTGCTGACAGTGCAGATAGTGGTCCTCTCCGTGCTACCGCACTGTGGGTACTTGCTGCTCCAGCAGGGCACGCACAG\n+>HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\n+GTCCTAGGTTGGGTCAATGATGAGAACCTTATAATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n+>HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]'..b'ME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\n+GGTTCCATAGTGTAGCGGTtATCACGTCTGCTTTACACGCAGAAGGtCCTGGGTTCGAGCCCCAGTGGAACCAcca\n+>NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\n+GTCTCTGTGGCGCAATCGGCtAGCGCGTTTGGCTGTTAACTAAAAAGtTGGTGGTTCGAACACACCCAGAGGCGcca\n+>NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\n+GTCTCTGTGGCGCAATCGGTtAGCGCATTCGGCTGTTAACCGAAAGGtTGGTGGTTCGAGCCCACCCAGGGACGcca\n+>NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\n+GGCAGTAAAGTAGGGTGGTtAAGACAAGGGGCTCTGGAGCAAGACTGCCCAAGATCAAATCCTGGTGCTGCCAcca\n+>NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\n+CCTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGATCCTTAGGtCGCTGGTTCGATTCCGGCTCGAAGGAcca\n+>NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\n+GGTTCCATAGTGTAGTGGTtATCACATCTGCTTTACACGCAGAAGGtCCTGGGTTCAAGCCCCAGTGGAACCAcca\n+>NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\n+GCAGCGATGGCCGAGTGGTtAAGGCGTTGGACTTGAAATCCAATGGGGTCTCCCCGCGCAGGTTCGAACCCTGCTCGCTGCGcca\n+>NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\n+GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCATGGGTTTGAGCCCCACGTTTGGTGcca\n+>NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\n+GGCAGAATGGTGCAGCGGTtcAGCACCCAGGCTCTGCAGCCAGCTGTTGCCTGGGCTCAAATCCCAGCTCTGCCAcca\n+>HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene 1&LOCI=[chr22:42471953-42472275:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008259&GENOME=hg19\n+ATTGTTGAACTATAGGGTATGAACTATAGGGTGTCCAGTGTACAGCATTTTATGGCTACTTGGTGTCACTCTAGAGCCACATAGCAAGTGGCTTCAAGAGGTAATTCTTGATCCTTTTGTAGTTCATGAGCGTGATGATTGGGTGTTCACATGCATGTGTGAGCTGTGCCACCCTCGAACCTTGTTACCATGTAGGCACATTACCGATCTGACATGAAGAAAAGAAAAGAAAAAAAAAGAAAAAGAGATAATTCTTTAGCTCAAGGGAGGAGTAAGACTTGACAGCTGTTGCGTTTCAGTATGTCTGGGCCTGATTATTTAAA\n+>HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\n+ATACGTGGCTGGGTTGCCATGCTCCATCTGCTGAGAGGCGTATTGTGAGTGGCAGGTGTTATGGATCACAGCCTCTGCATATGTGCCAGCAGAAAAAGTAATTGTAACCAGCAAAGCATTTTACTACATAAACGTTTTAGCCCCTATAAAAACATCCGGAGATCCTTTTGTTGTTCATGAGCATGACAATTGGGTGTTTTCATGCAGCGAGTGAGATGTGCCACCCTGGAACCTTGTTACGACGTCGCATGTTACCTGTCTGACCTGAAAAATAATTAATAAGTAAAACATACGGAAGCCAGTTTCTCATGGCTATTTCCAACTAGTCACTTGAAGAATATGGAATTAGTTATACAATTAGTTATACGTTGTATAACCATCATAAAATTAGTTACAGATTGATGTGACATTATCTTGAAATTAAT\n+>HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\n+GAGGGTTCTCAGCTTGAAGTTCCTTGTGCCTCTTTTAGGGAAGACACTCAGATGGTATATCGAGTATAAAATGACTTAGCGATTCTTCTCCTCAAAATGTGTCATTTATGATCCTTTTGTAGTTCATGAGTGTGATGATTGTGTGTTCATACGCTTGTGTGAGATGTGCCACCCTTGAACCTTGTTACGACATTGGCACATTACCCGTCTGATCTGAAAAAAAAAGTATCATTTATTTACTTACCTAAAATCTATGGAGTGCTTACTATGTGCCAAGTGCTTTTTAAAGCACTTGGAATACCTGACTGCATGAACAGAAACA\n+>HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\n+TGTATGTGGGAATGAATGATGACAAAATGTTTCAGTCCCAAATGATACATACTGATTATACCATTATATTTATCCTGACATTCCTCTAAGGCTTT\n+>HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\n+TGCCTCTAGGGGCTGGCTTTAGCTCAGCGGTTACTTCGACAATGCTTTCCATGGTTAGGAAACCAACCTCTCTGGGTGGTTTGAGACCCGTGGGCCCTCTCCAGTCCTTTTGTGGTCGCCA\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test1/ncrnadb09.v2.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1/ncrnadb09.v2.gtf Wed Jun 03 07:57:12 2015 -0400

[

b'@@ -0,0 +1,2269 @@\n+HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t1\t106\t.\t+\t.\n+HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t-\t.\n+HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t1\t116\t.\t-\t.\n+HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t+\t.\n+HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t-\t.\n+HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t1\t96\t.\t+\t.\n+HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t1\t115\t.\t+\t.\n+HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t+\t.\n+HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t+\t.\n+HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t-\t.\n+HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t1\t80\t.\t-\t.\n+HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t-\t.\n+HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t+\t.\n+HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t-\t.\n+HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t+\t.\n+HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t1\t92\t.\t+\t.\n+HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t1\t106\t.\t-\t.\n+HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t1\t153\t.\t-\t.\n+HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t1\t153\t.\t-\t.\n+HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t1\t123\t.\t-\t.\n+HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t-\t.\n+H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t+\t.\n+NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n+NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t+\t.\n+NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t-\t.\n+NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n+NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t-\t.\n+NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n+NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t-\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n+NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n+NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t+\t.\n+NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t1\t86\t.\t-\t.\n+NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t-\t.\n+NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t+\t.\n+NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t+\t.\n+NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n+NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t1\t86\t.\t+\t.\n+NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t-\t.\n+NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t-\t.\n+HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t1\t324\t.\t-\t.\n+HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t1\t426\t.\t+\t.\n+HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t1\t323\t.\t-\t.\n+HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t1\t96\t.\t+\t.\n+HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t1\t122\t.\t+\t.\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test1/snord81.bam

Binary file test-data/test1/snord81.bam has changed

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test1/snord81.flaimapper.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1/snord81.flaimapper.txt Wed Jun 03 07:57:12 2015 -0400

[

@@ -0,0 +1,4 @@
+Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total)
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_1 23 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 36 ATACATGATGATCTCAATCCAAC 70 29 99
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_2 22 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 67 CTCACTGATTACTTGATGACAA 97 74 171
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_3 26 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 79 TTACTTGATGACAATAAAATATCTGA 54 28 82

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test2/test_genomic_SE_reads.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2/test_genomic_SE_reads.fastqsanger Wed Jun 03 07:57:12 2015 -0400

@@ -0,0 +1,240 @@
+@read_001_fragment_1_chr1:120-148 (len=29)
+GGATAGTGCCAAAGCTCACTCACCACTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_002_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_003_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_004_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_005_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_006_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_007_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_008_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_009_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_010_fragment_1_chr1:120-149 (len=30)
+GGATAGTGCCAAAGCTCACTCACCACTGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_011_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_012_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_013_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_014_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_015_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_016_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_017_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_018_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_019_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_020_fragment_2_chr1:260-289 (len=30)
+GCTTACCTCTAGAATAAGTGTCAGCCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_021_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_022_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_023_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_024_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_025_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_026_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_027_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_028_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_029_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_030_fragment_3_chr1:400-429 (len=30)
+atacgtggcatttcaggaggcggccggagg
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_031_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_032_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_033_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_034_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_035_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_036_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_037_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_038_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_039_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_040_fragment_4_chr22:100-149 (len=50)
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_041_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_042_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_043_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_044_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_045_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_046_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_047_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_048_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_049_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_050_fragment_5_chr22:370-399 (len=30)
+TCTTGAGTGTTAAAATGTTGACCCCTGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_051_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_052_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_053_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_054_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_055_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_056_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_057_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_058_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_059_fragment_6_chrY:0-29 (len=30)
+TTGGGATGCGGGTAGTAGATGACTGCAGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_060_fragment_6_chrY:0-30 (len=31)
+TTGGGATGCGGGTAGTAGATGACTGCAGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test2/test_genomic_alignment.bam

Binary file test-data/test2/test_genomic_alignment.bam has changed

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test2/test_genomic_all_chromosomes.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2/test_genomic_all_chromosomes.fa Wed Jun 03 07:57:12 2015 -0400

@@ -0,0 +1,27 @@
+>chr1
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+TCTAGTGGTATGGTGGTATAGTAAGCTCGTACTGTGATACATGCGACAGG
+GGTAAGACCATCAGTAGTAGGGATAGTGCCAAAGCTCACTCACCACTGCC
+TATAAGGGGTGCTTACCTCTAGAATAAGTGTCAGCCAGTATAACCCCATG
+aagccgcgacacgacggctcacagccggtaagagtaaccccggagtgaac
+acctatggggctggataaaactgccctggtgaccgccatcaacaacccga
+atacgtggcatttcaggaggcggccggaggggggatgttttctactattc
+gaggccgttcgttataacttgttgcgttcctagccgctatatttgtctct
+GAGGCCGTTCGTTATAACTTGTTGCGTTCCTAGCCGCTATATTTGTCTCT
+TTGCCGACTAATGAGAACAACCACACCATAGCGATTTGACGCAGCGCCTC
+GGAATACCGTATCAGCAGGCGCCTCGTAAGGCCATTGCGAATACCAGGTA
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+>chr22
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+CTGGCTATGCACGAAGCAACTCTTGAGTGTTAAAATGTTGACCCCTGTAT
+>chrY
+TTGGGATGCGGGTAGTAGATGACTGCAGGGACTCCGACGTCAAGTACATT
+ACCCTCTCATAGGCGGCGTTCTAGATCACGTTACCGCCATATCATCCGAG
\ No newline at end of file

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test2/test_genomic_flaimapper_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2/test_genomic_flaimapper_output.txt Wed Jun 03 07:57:12 2015 -0400

@@ -0,0 +1,8 @@
+Fragment Size Reference sequence Start End Precursor Start in precursor End in precursor Sequence Corresponding-reads (start) Corresponding-reads (end) Corresponding-reads (total)
+ncRNA_1_chr1_Fragment_1 30 chr1 220 249 ncRNA_1 120 149 GGATAGTGCCAAAGCTCACTCACCACTGCC 10 9 19
+ncRNA_2_chr1_Fragment_1 30 chr1 220 249 ncRNA_2 20 49 GGATAGTGCCAAAGCTCACTCACCACTGCC 10 9 19
+ncRNA_2_chr1_Fragment_2 30 chr1 260 289 ncRNA_2 60 89 GCTTACCTCTAGAATAAGTGTCAGCCAGTA 10 10 20
+ncRNA_3_chr1_Fragment_1 30 chr1 400 429 ncRNA_3 50 79 atacgtggcatttcaggaggcggccggagg 10 10 20
+ncRNA_4_chr22_Fragment_1 50 chr22 100 149 ncRNA_4 0 49 AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA 10 10 20
+ncRNA_5_chr22_Fragment_1 30 chr22 370 399 ncRNA_5 170 199 TCTTGAGTGTTAAAATGTTGACCCCTGTAT 10 10 20
+ncRNA_6_chrY_Fragment_1 30 chrY 0 29 ncRNA_6 0 29 TTGGGATGCGGGTAGTAGATGACTGCAGGG 10 9 19

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test2/test_genomic_genes.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2/test_genomic_genes.gtf Wed Jun 03 07:57:12 2015 -0400

@@ -0,0 +1,6 @@
+chr1 flaimapper testing ncRNA 101 250 . + . gene_id="ncRNA_1"
+chr1 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_2"
+chr1 flaimapper testing ncRNA 351 500 . + . gene_id="ncRNA_3"
+chr22 flaimapper testing ncRNA 101 200 . + . gene_id="ncRNA_4"
+chr22 flaimapper testing ncRNA 201 400 . + . gene_id="ncRNA_5"
+chrY flaimapper testing ncRNA 1 100 . + . gene_id="ncRNA_6"
\ No newline at end of file

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test3/ncrnadb09.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3/ncrnadb09.fa Wed Jun 03 07:57:12 2015 -0400

[

diff -r d6abffbc9ee7 -r 96d135d3c57f test-data/test3/reference.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3/reference.gtf Wed Jun 03 07:57:12 2015 -0400

[

b'@@ -0,0 +1,2269 @@\n+HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t1\t105\t.\t.\t.\n+HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t.\t.\n+HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t1\t115\t.\t.\t.\n+HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n+HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n+HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t1\t95\t.\t.\t.\n+HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t1\t114\t.\t.\t.\n+HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t1\t104\t.\t.\t.\n+HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t1\t101\t.\t.\t.\n+HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t1\t103\t.\t.\t.\n+HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t1\t79\t.\t.\t.\n+HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t1\t90\t.\t.\t.\n+HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n+HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n+HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n+HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t1\t91\t.\t.\t.\n+HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t1\t105\t.\t.\t.\n+HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t1\t152\t.\t.\t.\n+HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t1\t152\t.\t.\t.\n+HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t1\t122\t.\t.\t.\n+HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t1\t102\t.\t.\t.\n+H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n+NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n+NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n+NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n+NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t.\t.\n+NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n+NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t1\t75\t.\t.\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n+NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t1\t74\t.\t.\t.\n+NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t1\t85\t.\t.\t.\n+NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n+NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t1\t77\t.\t.\t.\n+NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t1\t85\t.\t.\t.\n+NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t1\t76\t.\t.\t.\n+NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t1\t78\t.\t.\t.\n+HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t1\t323\t.\t.\t.\n+HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t1\t425\t.\t.\t.\n+HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t1\t322\t.\t.\t.\n+HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t1\t95\t.\t.\t.\n+HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t1\t121\t.\t.\t.\n'

diff -r d6abffbc9ee7 -r 96d135d3c57f tool_dependencies.xml
--- a/tool_dependencies.xml Thu May 21 07:26:46 2015 -0400
+++ b/tool_dependencies.xml Wed Jun 03 07:57:12 2015 -0400

@@ -1,39 +1,6 @@
<?xml version="1.0"?>
<tool_dependency>
- <package name="pysam" version="0.8.2.1">
- <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
- </package>
-
- <package name="flaimapper" version="1.1.5">
- <install version="1.0">
- <actions>
-
- <action type="set_environment_for_install">
- <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
- <package name="pysam" version="0.8.2.1" />
- </repository>
- </action>
-
- <action type="make_directory">$INSTALL_DIR</action>
- <action type="make_directory">$INSTALL_DIR/bin</action>
-
- <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.5-py2.7.egg"</action>
-
- <action type="set_environment">
- <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
- <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
- </action>
- </actions>
- </install>
-
- <readme>
- Because I accidentally included too much large files within the
- GitHub repository of FlaiMapper it is not convenient to use git
- to pull the latest code from. Downloading simply takes way to
- long and the package size is unnecessairy large.
-
- Instead, I have created an egg that can be installed using
- easy_install.
- </readme>
+ <package name="flaimapper" version="1.2.1">
+ <repository changeset_revision="88696b8f774b" name="package_flaimapper_1_2_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
</package>
</tool_dependency>