Galaxy |

Changeset 2:178ebdfe5a7e (2019-10-15)

Previous changeset 1:992c077f6e41 (2019-10-02) Next changeset 3:f6e3a10a88e5 (2020-04-25)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"

modified:
macros.xml

added:
umiout.sh
vpolo_convert.py

diff -r 992c077f6e41 -r 178ebdfe5a7e macros.xml
--- a/macros.xml Wed Oct 02 04:32:21 2019 -0400
+++ b/macros.xml Tue Oct 15 12:01:50 2019 -0400

@@ -1,5 +1,5 @@
<macros>
-    <token name="@VERSION@">0.14.1</token>
+    <token name="@VERSION@">0.14.1.2</token>
     <token name="@GALAXY_VERSION@">galaxy0</token>
     <token name="@IDX_VERSION@">q6</token>
     <xml name="requirements">
@@ -8,6 +8,10 @@
             <requirement type="package" version="1.2">seqtk</requirement>
             <requirement type="package" version="0.14.1">salmon</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="0.2.0">vpolo</requirement>
+            <requirement type="package" version="1.17.2">numpy</requirement>
+            <requirement type="package" version="0.25.1">pandas</requirement>
+            <requirement type="package" version="1.3.1">scipy</requirement>
         </requirements>
     </xml>
     <xml name="stranded">

diff -r 992c077f6e41 -r 178ebdfe5a7e old/README.rst
--- a/old/README.rst Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,62 +0,0 @@
-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 992c077f6e41 -r 178ebdfe5a7e old/static/images/ReadLibraryIllustration.png

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv
--- a/old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/hash.bin

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/header.json
--- a/old/test-data/cached_locally/prebuilt_index/header.json Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-{
-    "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 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/indexing.log
--- a/old/test-data/cached_locally/prebuilt_index/indexing.log Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,2 +0,0 @@
-[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 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/refInfo.json
--- a/old/test-data/cached_locally/prebuilt_index/refInfo.json Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/rsd.bin

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/sa.bin

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/txpInfo.bin

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/prebuilt_index/versionInfo.json
--- a/old/test-data/cached_locally/prebuilt_index/versionInfo.json Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/cached_locally/salmon_indexes_versioned.loc
--- a/old/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,33 +0,0 @@
-# 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 992c077f6e41 -r 178ebdfe5a7e old/test-data/gene_map.tab
--- a/old/test-data/gene_map.tab Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_1.fastq
--- a/old/test-data/reads_1.fastq Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,40000 +0,0 @@\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'

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_2.fastq
--- a/old/test-data/reads_2.fastq Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,40000 +0,0 @@\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 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_2.fastq.bz2

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_2.fastq.gz

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_both.fastq
--- a/old/test-data/reads_both.fastq Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,80000 +0,0 @@\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 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_both.fastq.bz2

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/reads_both.fastq.gz

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

diff -r 992c077f6e41 -r 178ebdfe5a7e old/test-data/salmon_genMap_result1.tab
--- a/old/test-data/salmon_genMap_result1.tab Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,5 +0,0 @@
-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 992c077f6e41 -r 178ebdfe5a7e old/test-data/salmon_quant_result1.tab
--- a/old/test-data/salmon_quant_result1.tab Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-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 992c077f6e41 -r 178ebdfe5a7e old/test-data/transcripts.fasta
--- a/old/test-data/transcripts.fasta Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,498 +0,0 @@\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 992c077f6e41 -r 178ebdfe5a7e old/tool-data/salmon_indexes_versioned.loc.sample
--- a/old/tool-data/salmon_indexes_versioned.loc.sample Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,32 +0,0 @@
-# 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 992c077f6e41 -r 178ebdfe5a7e old/tool_data_table_conf.xml.sample
--- a/old/tool_data_table_conf.xml.sample Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-<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 992c077f6e41 -r 178ebdfe5a7e old/tool_data_table_conf.xml.test
--- a/old/tool_data_table_conf.xml.test Wed Oct 02 04:32:21 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-<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 992c077f6e41 -r 178ebdfe5a7e umiout.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/umiout.sh Tue Oct 15 12:01:50 2019 -0400

@@ -0,0 +1,11 @@
+#!/usr/bin/bash
+
+mkdir fixed;
+for file in ./umiout/*;
+do prefix="${file%.dot.gz}";
+prefix=${prefix/.\/umiout\//};
+gunzip $file;
+sed "s/umiout\/$prefix.dot.gz/$prefix/" umiout/$prefix.dot > fixed/$prefix.dot;
+dot -Tpdf fixed/$prefix.dot -o fixed/$prefix.pdf;
+done
+ls fixed

diff -r 992c077f6e41 -r 178ebdfe5a7e vpolo_convert.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vpolo_convert.py Tue Oct 15 12:01:50 2019 -0400

@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+from vpolo.alevin import parser as par
+import argparse
+import os
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
+parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
+args = parser.parse_args()
+
+if args.mtx:
+    alevin_df = par.read_quants_bin("output")
+    with open("quants_mat.tsv", "w") as f:
+        f.write(alevin_df.to_csv(sep="\t"))
+
+if args.umi:
+    os.mkdir("umiout")
+    par.read_umi_graph("output", "umiout")