Repository 'pindel2vcf'
hg clone https://toolshed.g2.bx.psu.edu/repos/portiahollyoak/pindel2vcf

Changeset 0:f8f8dbf89999 (2016-05-17)
Commit message:
planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty
added:
pindel2vcf.xml
test-data/X_Hum1_D
test-data/X_Hum1_D.vcf
test-data/X_Hum1_D.vcf.idx
test-data/dm6.fa
test-data/igv.log
b
diff -r 000000000000 -r f8f8dbf89999 pindel2vcf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pindel2vcf.xml Tue May 17 05:02:35 2016 -0400
[
@@ -0,0 +1,46 @@
+<tool id="pindel2vcf" name="Pindel2Vcf" version="0.6.3">
+    <description>convert Pindel to VCF and index</description>
+    <requirements>
+        <requirement type="package" version="0.2.5b8">pindel</requirement>
+        <requirement type="package" version="0.2.3.48">igvtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+    pindel2vcf
+    -p "$input_file"
+    -r "$reference"
+    -R "$official_reference_name"
+    -d 00000000
+    -v "$input_file".vcf &&
+    mv "$input_file".vcf "$vcf_file"
+]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="txt" label="File to be converted"/>
+        <param name="reference" format="fasta" type="data" label="Reference genome in fasta format"/>
+        <param name="official_reference_name" type="text" label="Official Name for Reference Genome"/>
+    </inputs>
+    <outputs>
+        <data name="vcf_file" type="tabular" format="vcf" label="${input_file.name}.vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="X_Hum1_D" ftype="txt"/>
+            <param name="reference" value="dm6.fa" ftype="fasta"/>
+            <param name="official_reference_name" value="dmel_r6.10_FB2016_02" ftype="text"/>
+            <output name="vcf_file" file="X_Hum1_D.vcf" ftype="vcf"/>
+        </test>
+    </tests>
+    <help>
+        This tool converts Pindel output files to VCF format.
+        The following inputs are required:
+        - File(s) to be converted
+        - Reference genome in fasta format
+        - Official Name for Reference genome
+        - Date the reference genome was created
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1093/bioinformatics/btp394</citation>
+    </citations>
+</tool>
\ No newline at end of file
b
diff -r 000000000000 -r f8f8dbf89999 test-data/X_Hum1_D
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/X_Hum1_D Tue May 17 05:02:35 2016 -0400
b
b'@@ -0,0 +1,207150 @@\n+####################################################################################################\n+0\tD 1\tNT 0 ""\tChrID X\tBP 2678\t2680\tBP_range 2678\t2680\tSupports 5\t5\t+ 3\t3\t- 2\t2\tS1 12\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 72 72 3 3 2 2\n+TTCGACGAGCGCCTACAGCGAATTGCCGCTAAAACCTAAAAACAAAAAATTTATTAACAAATGAAATACAAATATACAAAATTCAAATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTGcACGCAACACATCCATATCCAACATAACAGACAAGAGGAGACGGGCCCTCAAACGTAAAACAATATCGCCAACTTTGCGCTTACAAACACAAAAAAATTTACAATTTTATGATGCCGTCTCCTCT\n+                                                                                      ATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTG ACGCAACACATCCATATCCA                                                                                                         \t+\t2541\t0\tX_HUM1\t@HWI-36691003/2\n+                                                                                      ATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTG ACGCAACACATCCATATCCAACAT                                                                                                     \t+\t2550\t0\tX_HUM1\t@HWI-18630759/1\n+                                                                                      ATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTG ACGCAACACATCCATATCCA                                                                                                         \t+\t2541\t0\tX_HUM1\t@HWI-2940085/1\n+                                                                              AAATTCAAATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTG ACGCAACACATCCATATCCAACATAACAGACAAGAGGAGACGGGCCCTCAAACGTAAAACAATATCGCCAACTTTGCG                                               \t-\t2994\t0\tX_HUM1\t@HWI-35723011/2\n+                                                                              AAATTCAAATAAAACAAAGCACTTACCTCACTGACCGCATCCAACTG ACGCAACACATCCATATCCAACATAACAGACAAGAGGAGACGGGCCCTCAAACGTAAAACAATATCGCCAACTTTGCG                                               \t-\t2994\t0\tX_HUM1\t@HWI-12975399/2\n+####################################################################################################\n+1\tD 51467\tNT 0 ""\tChrID X\tBP 3911\t55379\tBP_range 3911\t55383\tSupports 8\t8\t+ 8\t8\t- 0\t0\tS1 9\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 11 19 8 8 0 0\n+CAGACTATTTTTCCTCCCGAAAAACATACCTGGAAAACAAAAACAAGGCAACTATATAAACAAATAAATACATATATAATACTTACATCCAAACTACATTCCACCTAATGTATCTGAGAAATACAaaaat<51457>aatacAAAAATTACAGAAATCACAAAAATAAATAACAAATGCTATACTTACCTAATTTTAATATTACACCCATTCCCATGGCCCAATCTTTGGGCGGTCCCCAGCAACAATTC\n+                                                                                                           ATGTATCTGAGAAATACA                 AAAAATTAGAGAAATCACAAAAATAA                                                                                                   \t+\t3746\t0\tX_HUM1\t@HWI-34902444/1\n+                                                                                                       CCTAATGTATCTGAGAAATACA                 AAAAATTAGAGAAATCACAAAAATAA                                                                                                   \t+\t3746\t0\tX_HUM1\t@HWI-13892636/1\n+                                                                                                       CCTAATGTATCTGAGAAATACA                 AAAAATTAGAGAAATCACAAAAATAAAT                                                                                                 \t+\t3770\t0\tX_HUM1\t@HWI-1696698/1\n+                           ACCTGGAAAACAAAAACAAGGCAACTATATAAACAAATAAATACATATATAATACTTACATCCAAACTACATTCCACCTAATGTATCTGAGAAATACA                 AAAAATTAGAGAAATCACAAAAATAAA                                                                                                  \t+\t3813\t0\tX_HUM1\t@HWI-45525114/2\n+                          TACCTGGAAAACAAAAACAAGGCAACTATATAAACAAATAAATACATATATAATACTTACATCCAAACTACATTCCACCTAATGTATCTGAGAAATACA                 AAAAATTAGAGAAATCACAAAAATAA                                                                                                   \t+\t3812\t0\tX_HUM1\t@HWI-9492711/1\n+                          TACCTGGAAAACAAAAACAAGGCAACTATATAAACAAAT'..b'GAGACTCTTCACCT            AGACCAGCTGCGGATATTGGTACGGCCTGTTGAGAAGTTTGCGTGTCCCCACCATAAATTTTCAAGGTCCGAGGAGAAAATATCGACACAACATCTACCATATCTCTCTGCGAAAGACTTCCATG\n+                           ATCTCAATCTTCAGAGCCAATCCCTATCCCGAAGTTACGGATCTAATTTGCCGACTTCCCTTACCTACATTATTCTATCGACTAGAGACTCTTCACCTCCAAGGTTTCCAAGATCAGCTGCGGAT\t\t+\t23535326\t0\tX_HUM1\t@HWI-6457315/2\n+####################################################################################################\n+27307\tD 38\tNT 46 "CCAAGGTTTCCAAGATCAGCTGCGGATATTGGTACGGCCTGTTAGG"\tChrID X\tBP 23535502\t23535541\tBP_range 23535502\t23535541\tSupports 2\t2\t+ 1\t1\t- 1\t1\tS1 4\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 595 356 1 1 1 1\n+GTTATTGTTTCCCAATCAAGCCCGACTATCTCAATCTTCAGAGCCAATCCTTATCCCGAAGTTACGGATCTAATTTGCCGACTTCCCTTACCTACATTATTCTATCGACTAGAGACTCTTCACCT                                              AGTTTGCGTGTCCCCACCATAAATTTTCAAGGTCCGAGGAGAAAATATCGACACAACATCTACCATATCTCTCTGCGAAAGACTTCCATGATAGTACGGCTATAAAACAGAAAAGAAAACTCTTC\n+                                                                                            TACATTATTCTATCGACTAGAGACTCTTCACCTCCAAGGTTTCCAAGATCAGCTGCGGATATTGGTACGGCCTGTTAGGAGTTTGCGTGTCCTCACCATAAATTTTCAAGGTCCGAGGAGAAAAT\t\t-\t23535593\t0\tX_HUM1\t@HWI-28004328/1\n+                                                                                  TTCCCTTACCTACATTATTCTATCGACTAGAGACTCTTCACCTCCAAGGTTTCCAAGATCAGCTGCGGATATTGGTACGGCCTGTTAGGAGTTTGCGTGTCCTCACCATAAATTTTCAAGGTCCG\t\t+\t23535278\t0\tX_HUM1\t@HWI-10722982/2\n+####################################################################################################\n+27308\tD 18\tNT 1 "C"\tChrID X\tBP 23536830\t23536849\tBP_range 23536830\t23536849\tSupports 1\t1\t+ 1\t1\t- 0\t0\tS1 2\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 45 48 1 1 0 0\n+CATTTTACATAACTATATAGAACGCCCCGGGATTGTGTTAATTAGCTATAAATCGGTAAAAAACTAATCCCATTATTAGTCAAGTTAATTACGCTATTAGGTTCATATCCCAATAACTTGCACAT CGTGTTTCAAGACGGGTCCCGAAGGTATCCTGAATCTTTCGCATTGTTAATCATACAAACACAAAAATCGATGATAATTATGCCATTATGTAATTCCGAAAAAATAACGCACTGTAATCATATAA\n+                                                                        TTATTAGTCAAGTTAAGTACGCTATTAGGTTCATATCCCAATAACTTGCACATCCGTGTTTCAAGACGGGT\t\t+\t23536481\t0\tX_HUM1\t@HWI-14677898/2\n+####################################################################################################\n+27309\tD 22\tNT 6 "CTATCA"\tChrID X\tBP 23541691\t23541714\tBP_range 23541691\t23541714\tSupports 3\t3\t+ 2\t2\t- 1\t1\tS1 6\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 99 118 2 2 1 1\n+CGCGGAAACTACAACCATGGTAATAATAATAATAGCAGTGTGAGAATCGCGCAAAATACGTCGGAAAACTAACAGAACCCTTTAGGAAACAACCAATAAATGTAAAAGTTCATTCCATCAATTAT      TCTATAATCATTCAACTGAAAATAAACTAACATTTCTCATAGATACTGGTGCAGATATCTCACTTTTGAAAGTAAATTCTGATAACTTCATAATTCAAAATGAAAAAATAATAAACATCGAAGGC\n+                                                                                                                     TCAATTATCTATCATCTATAATCATTCAACTGAAAATAAACTAACATTTCTCATAGATACTGGTGCAGATATCTCACTTTTGAAAGTAAATTCTGATAACTTCAT\t\t+\t23541587\t0\tX_HUM1\t@HWI-41882528/2\n+                     AATAATAATAATAGCAGTGTGAGAATCGCGCAAAATACGTCGGAAAACTAACAGAACCCTTTAGGAAACAACCAATAAATGTAAAAGTTCATTCCATCAATTATCTATCATCTATAATCATTCAA\t\t+\t23541587\t0\tX_HUM1\t@HWI-41882528/1\n+                     AATAATAATAATAGCAGTGTGAGAATCGCGCAAAATACGTCGGAAAACTAACAGAACCCTTTAGGAAACAACCAATAAATGTAAAAGTTCATTCCATCAATTATCTATCATCTATAATCATTCAA\t\t-\t23541818\t0\tX_HUM1\t@HWI-41882528/1\n+####################################################################################################\n+27310\tD 6\tNT 5 "CAATC"\tChrID X\tBP 23541735\t23541742\tBP_range 23541735\t23541742\tSupports 1\t1\t+ 1\t1\t- 0\t0\tS1 2\tSUM_MS 0\t1\tNumSupSamples 1\t1\tX_HUM1 119 117 1 1 0 0\n+AATCGCGCAAAATACGTCGGAAAACTAACAGAACCCTTTAGGAAACAACCAATAAATGTAAAAGTTCATTCCATCAATTATAGTCTTAATATATTCGTAACCTTCTATAATCATTCAACTGAAAA     AACATTTCTCATAGATACTGGTGCAGATATCTCACTTTTGAAAGTAAATTCTGATAACTTCATAATTCAAAATGAAAAAATAATAAACATCGAAGGCATAGGCCAAGGAACAACCTTAATAGAAC\n+                                                                         TCAATTATAGTCTTAATATATTCGTAACCTTCTATAATCATTCAACTGAAAACAATCAACATTTCTCAT\t\t+\t23541488\t0\tX_HUM1\t@HWI-11615650/2\n'
b
diff -r 000000000000 -r f8f8dbf89999 test-data/X_Hum1_D.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/X_Hum1_D.vcf Tue May 17 05:02:35 2016 -0400
b
b'@@ -0,0 +1,27327 @@\n+##fileformat=VCFv4.0\n+##fileDate=00000000\n+##source=pindel\n+##reference=dmel_r6.10_FB2016_02\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">\n+##FORMAT=<ID=PL,Number=3,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">\n+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tX_HUM1\n+X\t484\t.\tGCTT\tGTC\t.\tPASS\tEND=487;HOMLEN=0;SVLEN=-3;SVTYPE=RPL;NTLEN=2\tGT:AD\t0/1:19,9\n+X\t2678\t.\tGC\tG\t.\tPASS\tEND=2679;HOMLEN=0;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:72,5\n+X\t3911\t.\tAAAAATTAGAGAAATCACAAAAATAAATAACAAAGGTTATACTTACCTAAAATTTAATATTACATCCATTCCCATGGCCCAATCGTTGCGGCGGTCCTCAGCAACAATTCCTGACCCGGAACATCCTAAAATAAAAGGCAAATAAAATAACACACATAAAATAGCAAACCTGACAGGCAAACTAGCAGATGCTAATTTGCAACACCATCCCGCTGACGTCACGCACGAAAATCCTTTCTCCAAGAGCGCAAAAACTGAAAAAAGAAACACAAGCTAACACTGGGAAATATATACTTCTTAACAAAATACTTATCTAAATTGCCAACCGGACGACTTCAAAGCTGCGGCCTAATTTTAATATTACATCTATCTCCGTGGCCCAATCTTTGCGGCGGTCCTCAGCAACAACTCCTGACCCGGAACATCCTAAAATAAAAAGAAAAACAAATAAGAATGCGACTCAAAATTAAGAAATAACACACAAAAAATAACAAACCTGACAGGCAAACTAGCAGATGCTAATTTGCAACACCATCATGCTGACGTCACGCACGAAAATCCTTTCTCCTAAGACCGCAAAAGCTGAAAAAGGAAACACAAGCTAATACTGGGAAATATATATTTTTAACAAAATACTTATCTAAACTGCCAAATTGACGACTTCAAAGCTGCGGCATCATAACTACAACGACCTCCAAAATAACTTTCAAAAAATGTACCTGAAAAACAGAAACTAATGAAATCATAAAAACAAATATAATACTTACCCCCAGATTAGCTATTACCTGAAAAACAAAAAATTAATGCAACTATATAAACAAATAAAAACAAATATACTTACCATCAAACTATCCATCACATTGTACCTGAAAACAAAAACAAATGCAATCATAAAAAACAATCCTAATGCAATACTTACCTATCTCTAACTTTACATTCATTTCCATGCCCGTATCGCTGCGGCGGACTTCTGCAACAAATCTTGAACCGGCGGCCCCAAGCTGCCAATCCCGACGCAATGGCCAATAGACGAGGCGCTCCTGGCAACTCTTGGCGAACAACTAAGCTGCATTCTACTGACGACTCCTCTGCCACAACGAGACAGATTCCTCCATTACGATCCCAGCAGCTTTAAGACCTTGTAACGACGGCTGCGCTGGACCCTCCTTGTTCTACCTTCTTTTGATGACCGGCGAAGTGGCCCTGCAAATTAACAATTTATCAAACAACTGCAATCATCTGCCACTGAGGTTGAAATATATACCTACTAAATGACAGCGGCGCGGGATACACTCACCTATAATAGGCTGCTTGCAGCGCTGGCCGGACATGCATATTGCAAGTGGCACGCATCCAGAGTCCACAACAAGCCCCAGCCAGAATGCCAAAATTACTCACCTGCAATGTTTCCTGAGGCCTCCAGCGACTCGGTGCTTCCGTCCTTCCGACGGGGGTACCTGAAAAGAATAAATCAATAACAATGTTAGTTTTAAATTTCAATGTTTTCTATAAAATCATTTCAATTGTAAATTGTAAACATACCATACAATATGATAATGTTACCTGTCCTAATTACTGTCAAAAGCCTAAGTCTACAAAATACTAACTACTTTTACATTATTACTAACTATGTCCAACCCCCAAACTCACCACATGTAATGTTACATTCAAAAATGCAAATTATTGTACCTATATATTACAAACTCTGTAATCAAAGGCAAAATAAATTGTGGATGCGGAACAGAATTTATTCTGTCTCCGTACCTCCACCAGCAAAGTTAAAAAAAAAAAAAAAAACCAGCAAAGTTAAAAAAATAATAAATAAAATAAAATTAAATAATTTAAACAAATAATAACAAATAATAAATAAATAATAAATTAAATAAATATTTAATAAAATAATCCGCGCTTTCCCTTGCTAAATATTCTGACGCGCAAATATAATTTAAATCGCCTTTTCTTTTTGACAAATTAAAAGTTTAAATATTGTCTTCCGGCCGCAAAGTTAAAACCGCGACAATAAAAAACAATTAATCGACAAACGAAAAGCGAACAATTACACTTGTGCAAAATCGACAAGCTGCCGTTATAACAAAAAGGAGACGAATAACCACAAAGAACTAAAGTTAAACTACCAGCAAAGTTAAAGCTCAAAGCAAGCTACAATATAAATTAAACAAATAAAATAAACGAATTAAATAAACTAATAATAAAACCTACTTAATAAAATAAACCGCGCTTTCACCTGCATAATTTTCTCACGCGCAAATTTAATTTAAATCGCCTCTTAGTATGAGAAATTAAAAGTTTAAAATTGTCTTCCGGCCGCCAAGTTAAAACCGCGACAACAATAAACATTTAGTGGACAAACTAAGGGTGAACAATTAATTGTGTAAAAATTGTGCAAATTGACAAGCTGCCGCCATAACCAAAAGGAAAAGAAAATCCATAGAGACGAAAAGAAGAAAGTCGACCGCAACCAGGAAGAGTTAAAAGGAGGAAAGGAGAAAGCC'..b'3532130\t.\tCCCGCCTCCCATGCGAG\tC\t.\tPASS\tEND=23532146;HOMLEN=1;HOMSEQ=C;SVLEN=-16;SVTYPE=DEL\tGT:AD\t0/0:337,11\n+X\t23532145\t.\tAGCGGTAGCAT\tATTACATTATGTAA\t.\tPASS\tEND=23532155;HOMLEN=0;SVLEN=-10;SVTYPE=RPL;NTLEN=13\tGT:AD\t0/0:392,3\n+X\t23532306\t.\tAAACGCGTGGGTTGTCT\tA\t.\tPASS\tEND=23532322;HOMLEN=3;HOMSEQ=AAC;SVLEN=-16;SVTYPE=DEL\tGT:AD\t0/0:82,8\n+X\t23532955\t.\tACGGTACACTT\tAGAAGTGTAC\t.\tPASS\tEND=23532965;HOMLEN=0;SVLEN=-10;SVTYPE=RPL;NTLEN=9\tGT:AD\t0/0:59,4\n+X\t23532997\t.\tAAACATTTGTCGGC\tA\t.\tPASS\tEND=23533010;HOMLEN=1;HOMSEQ=A;SVLEN=-13;SVTYPE=DEL\tGT:AD\t0/0:118,1\n+X\t23533010\t.\tCATTAAGTTTGAGGCCGACGATA\tCGTTTAAGTTGG\t.\tPASS\tEND=23533032;HOMLEN=0;SVLEN=-22;SVTYPE=RPL;NTLEN=11\tGT:AD\t0/0:121,1\n+X\t23533168\t.\tGT\tG\t.\tPASS\tEND=23533169;HOMLEN=1;HOMSEQ=T;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:88,1\n+X\t23533769\t.\tGA\tG\t.\tPASS\tEND=23533770;HOMLEN=1;HOMSEQ=A;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:19,3\n+X\t23533962\t.\tGCAA\tGGAAACTT\t.\tPASS\tEND=23533965;HOMLEN=0;SVLEN=-3;SVTYPE=RPL;NTLEN=7\tGT:AD\t0/0:38,1\n+X\t23534135\t.\tGTGGTTTCCTTTCCCTCGAGATGTGCCCTATCAATGA\tG\t.\tPASS\tEND=23534171;HOMLEN=6;HOMSEQ=TGGTTT;SVLEN=-36;SVTYPE=DEL\tGT:AD\t0/0:56,4\n+X\t23534143\t.\tCT\tC\t.\tPASS\tEND=23534144;HOMLEN=2;HOMSEQ=TT;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:53,2\n+X\t23534466\t.\tGTTGC\tG\t.\tPASS\tEND=23534470;HOMLEN=3;HOMSEQ=TTG;SVLEN=-4;SVTYPE=DEL\tGT:AD\t0/0:41,1\n+X\t23535021\t.\tAC\tA\t.\tPASS\tEND=23535022;HOMLEN=0;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:99,6\n+X\t23535502\t.\tTTGG\tTCCAAGGTTTCCA\t.\tPASS\tEND=23535505;HOMLEN=0;SVLEN=-3;SVTYPE=RPL;NTLEN=12\tGT:AD\t0/0:595,1\n+X\t23535502\t.\tTTGGAGACCAGCTGCGGATATTGGTACGGCCTGTTGAGA\tTCCAAGGTTTCCAAGATCAGCTGCGGATATTGGTACGGCCTGTTAGG\t.\tPASS\tEND=23535540;HOMLEN=0;SVLEN=-38;SVTYPE=RPL;NTLEN=46\tGT:AD\t0/0:595,2\n+X\t23536830\t.\tTATGTTAGACTCCTTGGTA\tTC\t.\tPASS\tEND=23536848;HOMLEN=0;SVLEN=-18;SVTYPE=RPL;NTLEN=1\tGT:AD\t0/0:48,1\n+X\t23537018\t.\tAAATGCAAGC\tA\t.\tPASS\tEND=23537027;HOMLEN=3;HOMSEQ=AAT;SVLEN=-9;SVTYPE=DEL\tGT:AD\t0/1:46,23\n+X\t23537106\t.\tGA\tG\t.\tPASS\tEND=23537107;HOMLEN=5;HOMSEQ=AAAAA;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:59,1\n+X\t23537555\t.\tATCCTCGTTAGTTTCTTT\tA\t.\tPASS\tEND=23537572;HOMLEN=5;HOMSEQ=TCCTC;SVLEN=-17;SVTYPE=DEL\tGT:AD\t0/0:73,1\n+X\t23537832\t.\tATTT\tA\t.\tPASS\tEND=23537835;HOMLEN=3;HOMSEQ=TTT;SVLEN=-3;SVTYPE=DEL\tGT:AD\t0/0:67,1\n+X\t23537890\t.\tCGTGAGATAAT\tC\t.\tPASS\tEND=23537900;HOMLEN=2;HOMSEQ=GT;SVLEN=-10;SVTYPE=DEL\tGT:AD\t0/0:51,1\n+X\t23539555\t.\tGCA\tG\t.\tPASS\tEND=23539557;HOMLEN=1;HOMSEQ=C;SVLEN=-2;SVTYPE=DEL\tGT:AD\t0/0:31,1\n+X\t23539795\t.\tAC\tA\t.\tPASS\tEND=23539796;HOMLEN=2;HOMSEQ=CC;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:127,1\n+X\t23539873\t.\tAT\tA\t.\tPASS\tEND=23539874;HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:68,3\n+X\t23539974\t.\tAT\tA\t.\tPASS\tEND=23539975;HOMLEN=8;HOMSEQ=TTTTTTTT;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:65,1\n+X\t23540207\t.\tTCA\tT\t.\tPASS\tEND=23540209;HOMLEN=4;HOMSEQ=CACA;SVLEN=-2;SVTYPE=DEL\tGT:AD\t0/0:56,2\n+X\t23540219\t.\tTATAAATGCGTTGTGG\tT\t.\tPASS\tEND=23540234;HOMLEN=2;HOMSEQ=AT;SVLEN=-15;SVTYPE=DEL\tGT:AD\t0/0:56,2\n+X\t23540352\t.\tAT\tA\t.\tPASS\tEND=23540353;HOMLEN=2;HOMSEQ=TT;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:38,2\n+X\t23540355\t.\tTA\tT\t.\tPASS\tEND=23540356;HOMLEN=11;HOMSEQ=AAAAAAAAAAA;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:56,2\n+X\t23540399\t.\tCTT\tC\t.\tPASS\tEND=23540401;HOMLEN=7;HOMSEQ=TTTTTTT;SVLEN=-2;SVTYPE=DEL\tGT:AD\t0/0:66,1\n+X\t23540480\t.\tTA\tT\t.\tPASS\tEND=23540481;HOMLEN=2;HOMSEQ=AA;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:47,1\n+X\t23540658\t.\tAAC\tA\t.\tPASS\tEND=23540660;HOMLEN=1;HOMSEQ=A;SVLEN=-2;SVTYPE=DEL\tGT:AD\t0/0:44,1\n+X\t23541495\t.\tGGCA\tG\t.\tPASS\tEND=23541498;HOMLEN=3;HOMSEQ=GCA;SVLEN=-3;SVTYPE=DEL\tGT:AD\t0/0:39,2\n+X\t23541641\t.\tGAACCCTTTAGGAAACAACCAATAAATGTAAAAGTTCATTCCATCAATTATA\tG\t.\tPASS\tEND=23541692;HOMLEN=0;SVLEN=-51;SVTYPE=DEL\tGT:AD\t0/0:99,1\n+X\t23541691\t.\tTAGTCTTAATATATTCGTAACCT\tTCTATCA\t.\tPASS\tEND=23541713;HOMLEN=0;SVLEN=-22;SVTYPE=RPL;NTLEN=6\tGT:AD\t0/0:118,3\n+X\t23541718\t.\tTAATCATTCAACTGAAAATA\tT\t.\tPASS\tEND=23541737;HOMLEN=2;HOMSEQ=AA;SVLEN=-19;SVTYPE=DEL\tGT:AD\t0/0:119,2\n+X\t23541731\t.\tGA\tG\t.\tPASS\tEND=23541732;HOMLEN=3;HOMSEQ=AAA;SVLEN=-1;SVTYPE=DEL\tGT:AD\t0/0:123,4\n+X\t23541735\t.\tATAAACT\tACAATC\t.\tPASS\tEND=23541741;HOMLEN=0;SVLEN=-6;SVTYPE=RPL;NTLEN=5\tGT:AD\t0/0:119,1\n'
b
diff -r 000000000000 -r f8f8dbf89999 test-data/X_Hum1_D.vcf.idx
b
Binary file test-data/X_Hum1_D.vcf.idx has changed
b
diff -r 000000000000 -r f8f8dbf89999 test-data/dm6.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dm6.fa Tue May 17 05:02:35 2016 -0400
b
b'@@ -0,0 +1,2877329 @@\n+>2L\n+Cgacaatgcacgacagaggaagcagaacagatatttagattgcctctcat\n+tttctctcccatattatagggagaaatatgatcgcgtatgcgagagtagt\n+gccaacatattgtgctctttgattttttggcaacccaaaatggtggcgga\n+tgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCA\n+TTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTG\n+CCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCG\n+CAAACCCAAAAAgacaatacacgacagagagagagagcagcggagatatt\n+tagattgcctattaaatatgatcgcgtatgcgagagtagtgccaacatat\n+tgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAA\n+ACCCAAatcgacaatgcacgacagaggaagcagaacagatatttagattg\n+cctctcattttctctcccatattatagggagaaatatgatcgcgtatgcg\n+agagtagtgccaacatattgtgctctttgattttttggcaacccaaaatg\n+gtggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAA\n+TAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGA\n+GAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTA\n+TATTACCGCAAACCCAAAAAgacaatacacgacagagagagagagcagcg\n+gagatatttagattgcctattaaatatgatcgcgtatgcgagagtagtgc\n+caacatattgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTT\n+TACCGCAAACCCAAatcgacaatgcacgacagaggaagcagaacagatat\n+ttagattgcctctcattttctctcccatattatagggagaaatatgatcg\n+cgtatgcgagagtagtgccaacatattgtgctctttgattttttggcaac\n+ccaaaatggtggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTA\n+ATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGC\n+GTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCT\n+CTGTCTTATATTACCGCAAACCCAAAAAgacaatacacgacagagagaga\n+gagcagcggagatatttagattgcctattaaatatgatcgcgtatgcgag\n+agtagtgccaacatattgtgctctCTATATAATGACTGCCTCTCATTCTG\n+TCTTATTTTACCGCAAACCCAAatcgacaatgcacgacagaggaagcaga\n+acagatatttagattgcctctcattttctctcccatattatagggagaaa\n+tatgatcgcgtatgcgagagtagtgccaacatattgtgctctttgatttt\n+ttggcaacccaaaatggtggcggatgaaCGAGATGATAATATATTCAAGT\n+TGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATAT\n+ATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCT\n+CTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAgacaatacacgaca\n+gagagagagagcagcggagatatttagattgcctattaaatatgatcgcg\n+tatgcgagagtagtgccaacatattgtgctctCTATATAATGACTGCCTC\n+TCATTCTGTCTTATTTTACCGCAAACCCAAatcgacaatgcacgacagag\n+gaagcagaacagatatttagattgcctctcattttctctcccatattata\n+gggagaaatatgatcgcgtatgcgagagtagtgccaacatattgtgctct\n+ttgattttttggcaacccaaaatggtggcggatgaaCGAGATGATAATAT\n+ATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAG\n+CACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAAT\n+GAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAgacaat\n+acacgacagagagagagagcagcggagatatttagattgcctattaaata\n+tgatcgcgtatgcgagagtagtgccaacatattgtgctctCTATATAATG\n+ACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAatcgacaatgca\n+cgacagaggaagcagaacagatatttagattgcctctcattttctctccc\n+atattatagggagaaatatgatcgcgtatgcgagagtagtgccaacatat\n+tgtgctctttgattttttggcaacccaaaatggtggcggatgaaCGAGAT\n+GATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTT\n+AAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATT\n+GTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAA\n+AAgacaatacacgacagagagagagagcagcggagatatttagattgcct\n+attaaatatgatcgcgtatgcgagagtagtgccaacatattgtgctctCT\n+ATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAatcg\n+acaatgcacgacagaggaagcagaacagatatttagattgcctctcattt\n+tctctcccatattatagggagaaatatgatcgcgtatgcgagagtagtgc\n+caacatattgtgctctttgattttttggcaacccaaaatggtggcggatg\n+aaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATT\n+GCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCC\n+AACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCA\n+AACCCAAAAAgacaatacacgacagagagagagagcagcggagatattta\n+gattgcctattaaatatgatcgcgtatgcgagagtagtgccaacatattg\n+tgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAAC\n+CCAAatcgacaatgcacgacagaggaagcagaacagatatttagattgcc\n+tctcattttctctcccatattatagggagaaatatgatcgcgtatgcgag\n+agtagtgccaacatattgtgctctttgattttttggcaacccaaaatggt\n+ggcggatgaaCGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATA\n+AATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGA\n+GTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATA\n+TTACCGCAAACCCAAAAAgacaatacacgacagagagagagagcagcgga\n+gatatttagattgcctattaaatatgatcgcgtatgcgagagtagtgcca\n+acatattgtgctctCTATATAATGACTGCCTCTCATTCTGTCTTATTTTA\n+CCGCAAACCCAAatcgacaatgcacgacagaggaagcagaacagatattt\n+agattgcctctcattttctctcccatattatagggagaaatatgatcgcg\n+tatgcgagagtagtgccaacatattgtgctctttgattttttggcaaccc\n+aaaatggtggcggatgaaC'..b'gggaccccatccg\n+gaagacagactggctgcaaatcaaatacacaggactggactactttgggc\n+cactgctggggactgtgtcccgtcacaaggagaagcgttgggtcgccttg\n+tttacgtgtttgacgacaagggcgattcacctgtagctggcgcatgacct\n+gtcgacggattcctgcataattgcgatcaggaacttcgtctgccgtagag\n+gggcggtatatagactgcgcagcgataacggcaagaacttcgtgggagct\n+gacagggaagccaggcgctttggcgacgtattcgagatggggaagcttca\n+gagtgagttgtcaagcagaagcattgaatgggtgtttaattgtccagcga\n+acccgtctgagggcagagtttgggagcgcatggtgcagtgcgtcaagaga\n+ttgaggcggagaatattgtaaactcgcgtgaaacattgaattcttccaga\n+ataaaacgtgttctactaccacggattagtctgccctttctttcgggaac\n+caatgtgtggggtagccgtttaaggcaactccctgtgacgcacgacgaca\n+gatacaatacaggattagtatcaagtactgtatttatattttctgttgtt\n+gtgttattttgttgttctatttgttgtgaattctcttttttatatttaac\n+aattagttttttgggaatgcctttatatttataaataaaatatagtaaaa\n+gtgtaagtattataatagcaagtatagttaatataataagttgtaatggg\n+ttgtatgtattagtgtgttcattaattatttctttagcatttagatatga\n+taatggttctaattttgttacattgttattgatatagaccgtttgtgtgt\n+agtctagtgttgtgcttgtaattaatatgttttctatttgaacagaacaa\n+ttaaaagcttttattatatggtctccttctattataatttctctattaat\n+tatacagttttgatttaatacaatttttgatattttccaagttaaaatta\n+tgtttggttctacataagttattccaatattgaatatccgcattctgttg\n+gtatttgatttaatattcctgtaattcatttgtttattattggttttcct\n+gagttttgtttgtaaacttgattatcttgaatataatacatttacatttt\n+ctataagtaatttattatctttgtctggatatggtacgatgttaaaaagt\n+gcagtttttataatgtctctaggaatatgggaaataataagtatttcatt\n+tgcatctgattttaaccacgtagaagtttttatatttagcaatttttcgg\n+aatttacatgtaataatggatcatgtcttaataatttgggattaaaaata\n+ccaagtcttgttaattgcataccaagttctatatcttcaatgtactaaac\n+taaactaaaagttctagtcttctgtcaccttcacttattgcgtttaaatg\n+gttgattacttcaatgcctctattgactacttctattacttcattcaatt\n+cattaatttgaatactatgttgagaaagatcgtatattttttgttctaat\n+tcttctttgtcattttgatctaaagtgccaaaaaggtatttatatgcggt\n+acctataaccgcttttattgagttttattattcttattccattcatttct\n+ctgtctaatttttcagttaaatattggatttgggctatagtaccatattc\n+ttcagcttgtttaattaaatttgcaaaagtttgttcggtctttgataagt\n+ttacggagaaatagtgatattcatagtttataggtatatNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNatgttcaactt\n+ttcttcctctatttgtttcttcgtaatgtttctcatctatttgttctacg\n+tgtcctgttttcttaaatgggttagttgttttactttttaccaatggtgc\n+ttgtttatatctagtatctacttcatagctatgtctatctttattcaact\n+tatctatttttaattgtttctctttttgggtgtcatatgcaggtgttcct\n+gcataaaggaaaatatcagctggtgttctcccagttgtattgtgtttagt\n+tttgtggttatatacatagagaatagtttcaaattgtgttatcttatttt\n+ctgggtcggactcactattaatgattcttaacttttcattgactgtttta\n+tggaatctttcaatttttacatttatacaacaacatttttacttgttgtg\n+atatttatattcacattctcggacttaagccataaatgtaacgcggaaca\n+tataaaagatgaatctttatcggcctttatttcggacggttttcccattt\n+cattgaaaattttaaggagagctctttttgcttccagccagtctctacta\n+ctgacttcaatcaaagcggcatattttgaataaatgtcaatgaatgagag\n+gaacgttttattattgattaaataaaaatctataacatatttttctctgg\n+gattagtatcttagtttagtatctctatgttctgttttggatatgttaca\n+tacttcgcattcattaataatgttctgtataaacttttggtagtctgggt\n+aataatatttttgtttaaaaagattagtttgttttctattcctcggtgta\n+aaagttctctgtgactttttataattatttctttaaattctgaatatgtt\n+tcaatgtcttttaatttgatgtttgatttcataactttagttatgttatt\n+cggactgacaatttctatgtaagcgttttgaaatgtaaggaaatctattt\n+cgttatgaaagaaaattacgattcttttggtacataaatattatttattt\n+aattctttggcaaggacatttgtcatttcta\n'