Galaxy |

Changeset 1:992c077f6e41 (2019-10-02)

Previous changeset 0:43658f594542 (2019-09-09) Next changeset 2:178ebdfe5a7e (2019-10-15)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"

modified:
macros.xml
test-data/cached_locally/salmon_indexes_versioned.loc

diff -r 43658f594542 -r 992c077f6e41 macros.xml
--- a/macros.xml Mon Sep 09 11:12:04 2019 -0400
+++ b/macros.xml Wed Oct 02 04:32:21 2019 -0400

@@ -1,7 +1,7 @@
<macros>
     <token name="@VERSION@">0.14.1</token>
     <token name="@GALAXY_VERSION@">galaxy0</token>
-    <token name="@IDX_VERSION@">q5</token>
+    <token name="@IDX_VERSION@">q6</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.0.6">bzip2</requirement>

diff -r 43658f594542 -r 992c077f6e41 old/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/README.rst Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,62 @@
+Galaxy wrappers for salmon
+=====================================
+
+These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors.
+All rights reserved. See the licence text below.
+
+Currently tested with salmon 0.11.2.
+
+
+Automated Installation
+======================
+
+Galaxy should be able to automatically install the salmon for you if you have Conda dependency management enabled in Galaxy.
+For more information please read the documentation at: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst
+
+
+History
+=======
+
+======== ======================================================================
+Version  Changes
+-------- ----------------------------------------------------------------------
+v0.6.3.0  - First release
+-------- ----------------------------------------------------------------------
+v0.7.2    - Second release
+-------- ----------------------------------------------------------------------
+v0.8.2    - Third release
+-------- ----------------------------------------------------------------------
+v0.9.1    - Fourth release
+-------- ----------------------------------------------------------------------
+v0.11.2   - Fifth release
+
+======== ======================================================================
+
+
+Bug Reports
+===========
+
+You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

diff -r 43658f594542 -r 992c077f6e41 old/static/images/ReadLibraryIllustration.png

Binary file old/static/images/ReadLibraryIllustration.png has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,1 @@
+RetainedTxp DuplicateTxp

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/hash.bin

Binary file old/test-data/cached_locally/prebuilt_index/hash.bin has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/header.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/prebuilt_index/header.json Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,14 @@
+{
+    "value0": {
+        "IndexType": 1,
+        "IndexVersion": "q5",
+        "UsesKmers": true,
+        "KmerLen": 31,
+        "BigSA": false,
+        "PerfectHash": false,
+        "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac",
+        "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04",
+        "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa",
+        "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33"
+    }
+}
\ No newline at end of file

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/indexing.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/prebuilt_index/indexing.log Wed Oct 02 04:32:21 2019 -0400

[

@@ -0,0 +1,2 @@
+[2019-07-25 13:45:20.599] [jLog] [info] building index
+[2019-07-25 13:45:20.654] [jLog] [info] done building index

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/refInfo.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/prebuilt_index/refInfo.json Wed Oct 02 04:32:21 2019 -0400

[

@@ -0,0 +1,5 @@
+{
+    "ReferenceFiles": [
+        "tools/salmon/test-data/transcripts.fasta"
+    ]
+}
\ No newline at end of file

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/rsd.bin

Binary file old/test-data/cached_locally/prebuilt_index/rsd.bin has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/sa.bin

Binary file old/test-data/cached_locally/prebuilt_index/sa.bin has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/txpInfo.bin

Binary file old/test-data/cached_locally/prebuilt_index/txpInfo.bin has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/prebuilt_index/versionInfo.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/prebuilt_index/versionInfo.json Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,6 @@
+{
+    "indexVersion": 2,
+    "hasAuxIndex": false,
+    "auxKmerLength": 31,
+    "indexType": 1
+}
\ No newline at end of file

diff -r 43658f594542 -r 992c077f6e41 old/test-data/cached_locally/salmon_indexes_versioned.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,33 @@
+# salmon_indexes_versioned.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Salmon.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path> <version>
+#
+# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5"
+
+
+
+# So, for example, if you had sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5
+#
+#
+hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5

diff -r 43658f594542 -r 992c077f6e41 old/test-data/gene_map.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/gene_map.tab Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,4 @@
+NM_174914 foo
+NM_001168316 bar
+NR_003084 baz
+NR_031764 foo

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/reads_1.fastq Wed Oct 02 04:32:21 2019 -0400

b'@@ -0,0 +1,40000 @@\n+@1:NM_014620:16:182\n+GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@17:NM_022658:1351:186\n+TCCATCAGGTTCCTAGAGAAAGTCAAGGGGGTTTTTCTAAGCAGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@18:NM_022658:1777:222\n+TAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@19:NM_018953:838:165\n+GCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@20:NM_022658:997:196\n+GGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@21:NM_022658:1639:210\n+TCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@22:NM_174914:42:131\n+TCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@23:NM_022658:782:137\n+TTCTTTTTTGCTTAGTCCTTGTTTTCTTCCTTTTCCTCCTCTTCTTTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@24:NM_022658:623:187\n+AGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@25:NM_022658:1061:175\n+GGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@26:NM_174914:1681:185\n+AGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@27:NM_022658:619:223\n+GGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@28:NM_022658:1432:199\n+GAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@29:NM_173860:122:191\n+CGCCGCCACCCTCGGCGCACGGCTCGCGGTAGTAACCCTTGCCGTCCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@30:NM_022658:1594:160\n+GCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@31:NM_153633:1041:170\n+ATTTCCCCTGAAATTCACCCAAGCCAGACCATCACACCTTGCAATATATA\n+'..b'IIIIIIIIIIIIIIIIIIIIIIII\n+@9971:NM_022658:1616:193\n+TTCTTTTTCAAGATTATTGCAGGTTCCCTTTAGGTAGTATGTTAAAGATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9972:NM_006897:924:149\n+ATATCTCAACACTGAACCCTCCCAAATCGCAAGAGTTTTCTTTTCCCCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9973:NM_174914:1854:200\n+GGAATCCATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9974:NM_022658:453:180\n+AGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9975:NM_022658:963:167\n+GTTTCTCCGTCTCCCCCCTCCAGCCCCCAAACAAATAAAGAGTGGGGGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9976:NM_014620:1302:181\n+GTTATGTTTTATAACCTGGTAATGTCCTCTGCCCGTTGCTGCTCCGGCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9977:NM_022658:175:88\n+CAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9978:NM_022658:57:146\n+GCCCAGTCCCGGGGAGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9979:NM_174914:1282:193\n+GGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9980:NM_014620:772:176\n+GGTGGTGGCCCGCCTGGGCCGGCCCGTGGCCTCGCGAATTGCCGGGCCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9981:NM_022658:184:203\n+CTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9982:NM_022658:1973:206\n+ATGACAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9983:NM_174914:435:160\n+CTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9984:NM_022658:470:179\n+TCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9985:NM_014620:1158:203\n+GGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_1.fastq.bz2

Binary file old/test-data/reads_1.fastq.bz2 has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_1.fastq.gz

Binary file old/test-data/reads_1.fastq.gz has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/reads_2.fastq Wed Oct 02 04:32:21 2019 -0400

b'@@ -0,0 +1,40000 @@\n+@1:NM_014620:16:182\n+CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+TGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@17:NM_022658:1351:186\n+AAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@18:NM_022658:1777:222\n+GGGTTTTCTTAGTGAAATAAGCAGCAACAAACGACAACAAAACCGCATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@19:NM_018953:838:165\n+CCTGCGGAGCTTGCCCTGGGCCCCGGGTACCGAGCTGAGCCGAGCTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@20:NM_022658:997:196\n+TTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@21:NM_022658:1639:210\n+TTTTTTTCTCCTATAGCAGGATTTTAAAATTTTTCTCTTTTTCTTTTTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@22:NM_174914:42:131\n+CCCTGTGCTTGAGAGTTCAGGGCCGGACACAGGCTCACAGGTCTCCACAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@23:NM_022658:782:137\n+ATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@24:NM_022658:623:187\n+CCTTGTTGTTCTCCTTTTTCCACTTCATCCTTCGGTTCTGGAACCAGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@25:NM_022658:1061:175\n+GAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@26:NM_174914:1681:185\n+ATCATGGATTCCTTAAAGAATGAGAACTTCGACATGGTGATAGTTGAAAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@27:NM_022658:619:223\n+CTTCTCCTCATCTCGGGCTCCCGGCAGTTTATCCTTGTTGTTCTCCTTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@28:NM_022658:1432:199\n+GGGATGGTTAGGTAGGATTTTAGAGGCGACTGCAGGCTCCTATCTACCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@29:NM_173860:122:191\n+GCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@30:NM_022658:1594:160\n+TTATTATTTTCGTGATTATGGTGATTTCTGAGCACTAACACTAATGCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@31:NM_153633:1041:170\n+CACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCT\n+'..b'IIIIIIIIIIIIIIIIIIIIIIII\n+@9971:NM_022658:1616:193\n+CTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9972:NM_006897:924:149\n+AACCCCACAAAATACCCCAACACAGGCGGGGGAGAGACGAAAAAGAAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9973:NM_174914:1854:200\n+TTAAAAAGGAAGAAAAATCATATCAAGTTATCAGTTGGCTTGCACCTGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9974:NM_022658:453:180\n+CACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCATGGAAACATGAGGCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9975:NM_022658:963:167\n+GTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9976:NM_014620:1302:181\n+GCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9977:NM_022658:175:88\n+GAACCGGCAGTCGTAATAGGCCGGTTCCAGGGACTCGCCGGCTTTGTATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9978:NM_022658:57:146\n+GGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACCCGCGGCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9979:NM_174914:1282:193\n+CTCTGCTTCCCAACACTGTTTATGTTGGAGGCTTGATGGAAAAACCTATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9980:NM_014620:772:176\n+ACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9981:NM_022658:184:203\n+AGTTGGAGATGCCGGAGGTGCCGTGGTGGAAGAAGTCTTGAACGTGGTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9982:NM_022658:1973:206\n+TGCTGCTTATTTCACTAAGAAAACCCAACAACTGAGACTGCCTAGCCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9983:NM_174914:435:160\n+TCTAGTCCTTCTAGTTATCTCCTGTTTTCTTGAAGAACAGGAAAAATGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9984:NM_022658:470:179\n+CTGTAAGTTTGCCGTCCACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9985:NM_014620:1158:203\n+CGGGGGTGCTGACCTGACTTTGGTGTTGGGGAGTCGGTGGTCCTTCTTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_2.fastq.bz2

Binary file old/test-data/reads_2.fastq.bz2 has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_2.fastq.gz

Binary file old/test-data/reads_2.fastq.gz has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_both.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/reads_both.fastq Wed Oct 02 04:32:21 2019 -0400

b'@@ -0,0 +1,80000 @@\n+@1:NM_014620:16:182\n+GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@1:NM_014620:16:182\n+CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n++\n+IIIIIIIII'..b'IIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_both.fastq.bz2

Binary file old/test-data/reads_both.fastq.bz2 has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/reads_both.fastq.gz

Binary file old/test-data/reads_both.fastq.gz has changed

diff -r 43658f594542 -r 992c077f6e41 old/test-data/salmon_genMap_result1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/salmon_genMap_result1.tab Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,5 @@
+Name Length EffectiveLength TPM NumReads
+baz 1640 1052.77 1.09566 0.00943897
+NR_031764 1853 1214.33 10407.1 103.415
+foo 348.949 235.269 976889 9737.65
+bar 2283 1528.95 12702.4 158.926

diff -r 43658f594542 -r 992c077f6e41 old/test-data/salmon_quant_result1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/salmon_quant_result1.tab Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,16 @@
+Name Length EffectiveLength TPM NumReads
+NM_001168316 2283 2106.09 12428 158.641
+NM_174914 2385 2208.09 112348 1503.55
+NR_031764 1853 1676.09 10021.5 101.805
+NM_004503 1681 1504.09 36259.8 330.551
+NM_006897 1541 1364.09 80313.1 664
+NM_014212 2037 1860.09 4878.54 55
+NM_014620 2300 2123.09 45879.2 590.368
+NM_017409 1959 1782.09 4351.4 47
+NM_017410 2396 2219.09 3122.74 42
+NM_018953 1612 1435.09 26213 228
+NM_022658 2288 2111.09 381473 4881
+NM_153633 1666 1489.09 40073.1 361.67
+NM_153693 2072 1895.09 6478.45 74.4115
+NM_173860 849 672.091 236161 962
+NR_003084 1640 1463.09 0.00490872 4.3529e-05

diff -r 43658f594542 -r 992c077f6e41 old/test-data/transcripts.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/test-data/transcripts.fasta Wed Oct 02 04:32:21 2019 -0400

b'@@ -0,0 +1,498 @@\n+>NM_001168316\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCC\n+TTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCT\n+GCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGT\n+CAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGA\n+GCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAA\n+AGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATC\n+CATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATT\n+TAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACT\n+CTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTT\n+TTCTTCCTTTTTAAAATCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAG\n+GACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTC\n+TACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGT\n+GCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAG\n+TCT\n+>NM_174914\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGA'..b'G\n+GATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAG\n+GACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGC\n+CCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACA\n+GTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGA\n+CCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCG\n+AGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCC\n+GGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGG\n+CCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGC\n+AGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCAC\n+CAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATT\n+CCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCC\n+TCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTT\n+CTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTC\n+AGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCA\n+CCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCC\n+TCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCC\n+CACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGC\n+CCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTG\n+TGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGT\n+TTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACA\n+AAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAA\n+ATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATAT\n+TTAATAAAACTGATATTATTTTTAAAACTTTA\n+>NM_173860\n+ATGGGCGAGCATAATCTCCTGAATCCCGGGTTTGTGGGGCCGCTGGTAAACATCCACACG\n+GGAGACACCTTCTACTTCCCCAACTTCCGCGCGTCCGGGGCGCAGCTTCCCGGGCTGCCT\n+TCGCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGGCGGAGCCG\n+TGCAATGGCTACCCGCAGCCCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGC\n+CGCACGTGCGAGCTGGCGCGCGTGGAGGACGGCAAGGGTTACTACCGCGAGCCGTGCGCC\n+GAGGGTGGCGGCGGGGGCCTGAAGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCC\n+GGGGCAGCGCTGCTCCCGCTGGAGCCGTCGGGGCCGCCTGCGCTCGGCTTCAAGTACGAC\n+TACGCGGCGGGCGGCGGCGGTGGCGACGGCGGCGGCGGCGCAGGACCTCCGCACGACCCG\n+CCCTCCTGCCAGTCGCTGGAATCCGACTCCAGTTCGTCCCTGCTCAACGAGGGCAACAAG\n+GGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTATCGCCGTTGAACCCCGGCGGCGGGCTC\n+TCGGCCAGCGGCGCGCCCTGGTACCCGATCAACAGCCGCTCTCGGAAGAAGCGCAAGCCC\n+TATTCGAAGTTGCAACTGGCAGAGCTGGAGGGCGAGTTTCTGGTCAACGAGTTCATCACA\n+CGCCAGCGCCGGAGGGAACTCTCAGACCGCTTGAATCTTAGTGACCAGCAGGTCAAGATC\n+TGGTTTCAGAACCGGAGAATGAAAAAGAAAAGACTTCTGTTGAGGGAGCAAGCTCTCTCC\n+TTCTTTTAA\n+>NR_003084\n+TTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAAC\n+CATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAA\n+TCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGA\n+AGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCT\n+CTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTT\n+GAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCC\n+CTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTT\n+TGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCAC\n+AGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAG\n+AGTGACAGCAGCGCTCGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCA\n+GACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCAT\n+AGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCG\n+CAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCG\n+GGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCC\n+TTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCAC\n+AGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGC\n+TGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCA\n+AGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGG\n+CCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCG\n+GCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCT\n+GGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTT\n+GTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGC\n+CTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCC\n+AAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCA\n+GCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTA\n+GAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGC\n+TGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAA\n+TAAAGAGAGAACAGGACTAA\n'

diff -r 43658f594542 -r 992c077f6e41 old/tool-data/salmon_indexes_versioned.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/tool-data/salmon_indexes_versioned.loc.sample Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,32 @@
+# salmon_indexes_versioned.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Salmon.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path> <version>
+#
+# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5"
+
+
+
+# So, for example, if you had sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5
+#
+#

diff -r 43658f594542 -r 992c077f6e41 old/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/tool_data_table_conf.xml.sample Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,7 @@
+<tables>
+    
+    <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, version</columns>
+        <file path="tool-data/salmon_indexes_versioned.loc" />
+    </table>
+</tables>

diff -r 43658f594542 -r 992c077f6e41 old/tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/old/tool_data_table_conf.xml.test Wed Oct 02 04:32:21 2019 -0400

@@ -0,0 +1,7 @@
+<tables>
+    
+    <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, version</columns>
+        <file path="${__HERE__}/test-data/cached_locally/salmon_indexes_versioned.loc" />
+    </table>
+</tables>

diff -r 43658f594542 -r 992c077f6e41 test-data/cached_locally/salmon_indexes_versioned.loc
--- a/test-data/cached_locally/salmon_indexes_versioned.loc Mon Sep 09 11:12:04 2019 -0400
+++ b/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:32:21 2019 -0400

@@ -30,4 +30,4 @@
#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5
#
#
-hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5
+hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q6