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Changeset 5:4e9b6a0fcb78 (2017-08-05)

Previous changeset 4:d44bd2602944 (2017-07-10) Next changeset 6:de61aa230275 (2018-10-30)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

modified:
generate_test_data.sh
macros.xml
upgma_cluster.xml

added:
test-data/extract_barcodes/inseqs.fastq
test-data/extract_barcodes/inseqs_R1.fastq
test-data/extract_barcodes/inseqs_R2.fastq
test-data/extract_barcodes/mapping_data.txt
test-data/split_libraries_fastq/lane1_barcode.fastq.gz
test-data/split_libraries_fastq/lane1_read1.fastq.gz
test-data/split_libraries_fastq/lane2_barcode.fastq
test-data/split_libraries_fastq/lane2_barcode.fastq.gz
test-data/split_libraries_fastq/lane2_read1.fastq
test-data/split_libraries_fastq/lane2_read1.fastq.gz
test-data/split_libraries_fastq/map.txt

diff -r d44bd2602944 -r 4e9b6a0fcb78 generate_test_data.sh
--- a/generate_test_data.sh Mon Jul 10 16:44:06 2017 -0400
+++ b/generate_test_data.sh Sat Aug 05 07:33:48 2017 -0400

@@ -228,6 +228,54 @@
     --suppress_group_significance
rm -rf core_diversity_analyses_2

+# extract_barcodes
+extract_barcodes.py \
+    --fastq1 'test-data/extract_barcodes/inseqs.fastq' \
+    --input_type 'barcode_single_end' \
+    -o extract_barcodes_1 \
+    --bc1_len '6' \
+    --rev_comp_bc1
+rm -rf extract_barcodes_1
+
+extract_barcodes.py \
+    --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
+    --input_type 'barcode_paired_end' \
+    --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
+    -o extract_barcodes_2 \
+    --bc1_len '6' \
+    --bc2_len '6'
+rm -rf extract_barcodes_2
+
+extract_barcodes.py \
+    --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
+    --input_type 'barcode_paired_end' \
+    --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
+    -o extract_barcodes_3 \
+    --bc1_len '6' \
+    --bc2_len '6' \
+    --mapping_fp 'test-data/extract_barcodes/mapping_data.txt' \
+    --attempt_read_reorientation \
+    --disable_header_match
+rm -rf extract_barcodes_3
+
+extract_barcodes.py \
+    --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
+    --input_type 'barcode_paired_stitched' \
+    -o extract_barcodes_4 \
+    --bc1_len '6' \
+    --bc2_len '8' \
+    --rev_comp_bc1 \
+    --rev_comp_bc2
+rm -rf extract_barcodes_4
+
+extract_barcodes.py \
+    --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
+    --input_type 'barcode_in_label' \
+    --char_delineator '#' \
+    -o extract_barcodes_5 \
+    --bc1_len '6'
+rm -rf extract_barcodes_5
+
# filter_alignment
filter_alignment.py \
     --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
@@ -943,23 +991,79 @@

# split_libraries_fastq
split_libraries_fastq.py \
-    --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \
-    -o split_libraries \
-    --mapping_fps 'test-data/map.tsv' \
-    --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \
+    --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
+    -o split_libraries_1 \
+    --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
+    --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
+    --max_bad_run_length 3 \
+    --min_per_read_length_fraction 0.75 \
+    --sequence_max_n 0 \
+    --start_seq_id 0 \
+    --rev_comp_mapping_barcodes \
+    --phred_quality_threshold 19 \
+    --barcode_type 'golay_12' \
+    --max_barcode_errors 1.5
+rm -rf split_libraries_1
+
+split_libraries_fastq.py \
+    --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
+    -o split_libraries_2 \
+    --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
+    --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
     --store_qual_scores \
     --store_demultiplexed_fastq \
     --max_bad_run_length 3 \
     --min_per_read_length_fraction 0.75 \
     --sequence_max_n 0 \
     --start_seq_id 0 \
+    --rev_comp_mapping_barcodes \
+    --phred_quality_threshold 19 \
+    --barcode_type 'golay_12' \
+    --max_barcode_errors 1.5
+rm -rf split_libraries_2
+
+split_libraries_fastq.py \
+    --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
+    -o split_libraries_3 \
+    --mapping_fps 'test-data/split_libraries_fastq/map.txt,test-data/split_libraries_fastq/map.txt' \
+    --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz,test-data/split_libraries_fastq/lane2_barcode.fastq.gz' \
+    --max_bad_run_length 3 \
+    --min_per_read_length_fraction 0.75 \
+    --sequence_max_n 0 \
+    --start_seq_id 0 \
+    --rev_comp_mapping_barcodes \
+    --phred_quality_threshold 19 \
     --barcode_type 'golay_12' \
     --max_barcode_errors 1.5
-cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular'
-cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta'
-cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual'
-cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq'
-rm -rf split_libraries
+rm -rf split_libraries_3
+
+split_libraries_fastq.py \
+    --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
+    -o split_libraries_4 \
+    --sample_ids 'my.sample.1' \
+    --max_bad_run_length 3 \
+    --min_per_read_length_fraction 0.75 \
+    --sequence_max_n 0 \
+    --start_seq_id 0 \
+    --rev_comp_mapping_barcodes \
+    --phred_quality_threshold 19 \
+    --barcode_type 'not-barcoded' \
+    --max_barcode_errors 1.5
+rm -rf split_libraries_4
+
+split_libraries_fastq.py \
+    --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
+    -o split_libraries_5 \
+    --sample_ids 'my.sample.1,my.sample.2' \
+    --max_bad_run_length 3 \
+    --min_per_read_length_fraction 0.75 \
+    --sequence_max_n 0 \
+    --start_seq_id 0 \
+    --rev_comp_mapping_barcodes \
+    --phred_quality_threshold 19 \
+    --barcode_type 'not-barcoded' \
+    --max_barcode_errors 1.5
+rm -rf split_libraries_5

# summarize_taxa
cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'

diff -r d44bd2602944 -r 4e9b6a0fcb78 macros.xml
--- a/macros.xml Mon Jul 10 16:44:06 2017 -0400
+++ b/macros.xml Sat Aug 05 07:33:48 2017 -0400

@@ -33,7 +33,7 @@
                 <option value="history">The active history</option>
             </param>
             <when value="cached">
-                <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select">
+                <param argument="--reference_seqs_fp" type="select" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)">
                     <options from_data_table="qiime_rep_set"/>
                 </param>
             </when>

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/extract_barcodes/inseqs.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_barcodes/inseqs.fastq Sat Aug 05 07:33:48 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+NACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGG
++
+#1=DDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDB@B8?;@AAB?<?7<75;CCB##################################
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/extract_barcodes/inseqs_R1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_barcodes/inseqs_R1.fastq Sat Aug 05 07:33:48 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:#NACGGA
+NACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGG
++
+#1=DDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDB@B8?;@AAB?<?7<75;CCB##################################
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:#NACGGG
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/extract_barcodes/inseqs_R2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_barcodes/inseqs_R2.fastq Sat Aug 05 07:33:48 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 2:N:0:#NACGGA
+TCGTCGATAATCA
++
+====ADDDHFHHF
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:#NACGGG
+ACGTGTACCCAAA
++
+@CCFFFDEHHHGF
\ No newline at end of file

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/extract_barcodes/mapping_data.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_barcodes/mapping_data.txt Sat Aug 05 07:33:48 2017 -0400

@@ -0,0 +1,3 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType Year Month
+L1S8 NACGGATCGTCG GTGCCAGCMGCCGCGGTAA gut 2008 10
+L1S140 NACGGGACGTGT GTGCCAGCMGCCGCGGTAA gut 2008 10
\ No newline at end of file

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/barcodes.fastq
--- a/test-data/split_libraries_fastq/barcodes.fastq Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1000 +0,0 @@\n-@HWI-EAS440_0386:1:23:17547:1423#0/1\n-ATGCAGCTCAGT\n-+\n-hhhhhhhhhhhg\n-@HWI-EAS440_0386:1:23:14818:1533#0/1\n-CCCCTCAGCGGC\n-+\n-ccc_c^_a[[JN\n-@HWI-EAS440_0386:1:23:14401:1629#0/1\n-GACGAGTCAGTC\n-+\n-ffdfcfffffcf\n-@HWI-EAS440_0386:1:23:15259:1649#0/1\n-AGCAGTCGCGAT\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:13748:2482#0/1\n-AGCACACCTACA\n-+\n-ffffaffddffc\n-@HWI-EAS440_0386:1:23:6532:3028#0/1\n-GAGAGAATGATC\n-+\n-ghhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:8677:3027#0/1\n-CACAGTGGACGT\n-+\n-eggggggggggg\n-@HWI-EAS440_0386:1:23:5678:3052#0/1\n-ATAGCTCCATAC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:11889:3171#0/1\n-ACGTTAGCACAC\n-+\n-hhhhhhfhhhhh\n-@HWI-EAS440_0386:1:23:2112:3374#0/1\n-GAGAGAATGATC\n-+\n-eddaabddddcf\n-@HWI-EAS440_0386:1:23:5900:3393#0/1\n-AGGTGTGATCGC\n-+\n-fffefhhhhggh\n-@HWI-EAS440_0386:1:23:15468:3455#0/1\n-GAGAATACGTGA\n-+\n-ehghghfhhggg\n-@HWI-EAS440_0386:1:23:4405:3490#0/1\n-ACGCGCAGATAC\n-+\n-fffffaffffaf\n-@HWI-EAS440_0386:1:23:4674:3593#0/1\n-ACATTCAGCGCA\n-+\n-fggggggggggg\n-@HWI-EAS440_0386:1:23:15912:3842#0/1\n-ATCAGGCGTGTG\n-+\n-ccggggcgggff\n-@HWI-EAS440_0386:1:23:15732:4249#0/1\n-CTCATGTACAGT\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:17444:4527#0/1\n-AACGCACGCTAG\n-+\n-hhhhghhhhhhh\n-@HWI-EAS440_0386:1:23:10725:4873#0/1\n-AACGCACGCTAG\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:23:11691:4945#0/1\n-ATCTTAGACTGC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:4723:5217#0/1\n-CTCGCACATATA\n-+\n-\\acaYW^^aYYV\n-@HWI-EAS440_0386:1:23:13608:5705#0/1\n-GATCGTCCAGAT\n-+\n-chhhdhhhgheh\n-@HWI-EAS440_0386:1:23:5195:5979#0/1\n-CAGCAGCACATA\n-+\n-ggggggggggg_\n-@HWI-EAS440_0386:1:23:1372:6057#0/1\n-AGCTCTCAGAGG\n-+\n-\\aab`_ccc^ff\n-@HWI-EAS440_0386:1:23:2305:6385#0/1\n-CGTATCTGCGAA\n-+\n-hhhhhhhhhghh\n-@HWI-EAS440_0386:1:23:17333:6563#0/1\n-CCAGTGTATGCA\n-+\n-ggffgggggegg\n-@HWI-EAS440_0386:1:23:1091:6583#0/1\n-CGATGCACCAGA\n-+\n-c^ca_\\\\_]``a\n-@HWI-EAS440_0386:1:23:16169:6630#0/1\n-CAACTATCAGCT\n-+\n-hhhhhfhhhhhh\n-@HWI-EAS440_0386:1:23:14554:7030#0/1\n-AGTTAGTGCGTC\n-+\n-hhhhhghhhhhh\n-@HWI-EAS440_0386:1:23:14518:7351#0/1\n-CTCGCACATATA\n-+\n-gfgggggggggg\n-@HWI-EAS440_0386:1:23:17440:7360#0/1\n-GCTGCTGCAATA\n-+\n-ggggfggggggf\n-@HWI-EAS440_0386:1:23:11290:7687#0/1\n-ATCGTACAACTC\n-+\n-hhhfhhhhhhhh\n-@HWI-EAS440_0386:1:23:1465:8235#0/1\n-CACATCTAACAC\n-+\n-cc^ccccccccc\n-@HWI-EAS440_0386:1:23:3176:8324#0/1\n-ACTGATCCTAGT\n-+\n-add^dcda^ddd\n-@HWI-EAS440_0386:1:23:12535:8807#0/1\n-GAAGCTACTGTC\n-+\n-hhfhhhhhhhhh\n-@HWI-EAS440_0386:1:23:14562:8883#0/1\n-CGAGTTGTAGCG\n-+\n-fhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:5451:9226#0/1\n-AGATACACGCGC\n-+\n-hhhhghhhhhhh\n-@HWI-EAS440_0386:1:23:19204:9448#0/1\n-GATCGCAGGTGT\n-+\n-cccccc_ccTWU\n-@HWI-EAS440_0386:1:23:13161:10184#0/1\n-CTACATCTAAGC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:19192:10519#0/1\n-CATCGTATCAAC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:17370:10963#0/1\n-GCTCAGTGCAGA\n-+\n-gffggggfgggg\n-@HWI-EAS440_0386:1:23:8386:11532#0/1\n-CAGCTAGAACGC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:23:10215:11663#0/1\n-AGATCGGCTCGA\n-+\n-ffffffffffcW\n-@HWI-EAS440_0386:1:23:15454:11726#0/1\n-ACGTACTCAGTG\n-+\n-ggggggggggff\n-@HWI-EAS440_0386:1:23:6589:11781#0/1\n-AGTACGCTCGAG\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:23:3256:12101#0/1\n-ATGCCTGAGCAG\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:23:5860:12157#0/1\n-ACATGTCACGTG\n-+\n-hhhghhhhhhhh\n-@HWI-EAS440_0386:1:23:8148:12187#0/1\n-AACTGTGCGTAC\n-+\n-hhghhhhhhhhh\n-@HWI-EAS440_0386:1:23:14399:12333#0/1\n-ACATGATCGTTC\n-+\n-ZTPQFILLJJKK\n-@HWI-EAS440_0386:1:23:6966:12378#0/1\n-CATACCAGTAGC\n-+\n-\\aa_aaa^aa\\^\n-@HWI-EAS440_0386:1:23:5056:12637#0/1\n-CGCATGAGGATC\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:23:2628:12653#0/1\n-ACGCTCATGGAT\n-+\n-cccccccccccc\n-@HWI-EAS440_0386:1:23:3303:12826#0/1\n-AGGTGTGATCGC\n-+\n-hffhhhhhhhhh\n-@HWI-EAS440_0386:1:23:11685:12866#0/1\n-CTCCACATGAGA\n-+\n-hhhhghhhhchh\n-@HWI-EAS440_0386:1:23:3932:12883#0/1\n-CTACTGATATCG\n-+\n-aZ]]]\\Sa^a]_\n-@HWI-EAS440_0386:1:23:3535:13218#0/1\n-ACGACGTCTTAG\n-+\n-hhhhghhhhhhh\n-@HWI-EAS440_0386:1:23:6909:13409#0/1\n-AGTTCAGACGCT\n-+\n-gggggfgggggg\n-@HWI-EAS440_0386:1:23:6191:13528#0/1\n-GCTCAGTGCAGA\n-+\n-ggggggeggggg\n-@HWI-EAS440_0386:1:23:17158:13561#0/1\n-AATCGTGACTCG\n-+'..b'/1\n-ACTACGTGTGGT\n-+\n-hhhhhhhhhghg\n-@HWI-EAS440_0386:1:25:2027:2951#0/1\n-AGCTGACTAGTC\n-+\n-gcggggeggfdf\n-@HWI-EAS440_0386:1:25:13175:2941#0/1\n-GCTGCTGCAATA\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:13489:2951#0/1\n-AGCTGACTAGTC\n-+\n-hhhhfhhhhhhh\n-@HWI-EAS440_0386:1:25:6132:2959#0/1\n-ACTACGTGTGGT\n-+\n-a`aY]ada^e\\L\n-@HWI-EAS440_0386:1:25:2692:2971#0/1\n-ACACACTATGGC\n-+\n-hhghhhhhhfhh\n-@HWI-EAS440_0386:1:25:1831:2983#0/1\n-ACACACTATGGC\n-+\n-ggggcggacg^[\n-@HWI-EAS440_0386:1:25:6335:2989#0/1\n-CCTCTCGTGATC\n-+\n-afdeff\\ffaca\n-@HWI-EAS440_0386:1:25:10162:3028#0/1\n-ATGGCAGCTCTA\n-+\n-fffffdfRc]^[\n-@HWI-EAS440_0386:1:25:4348:3042#0/1\n-ATGGCAGCTCTA\n-+\n-ffa_fffa_d\\J\n-@HWI-EAS440_0386:1:25:5972:3048#0/1\n-CTGAGATACGCG\n-+\n-hhhhhfhhhghh\n-@HWI-EAS440_0386:1:25:9861:3050#0/1\n-ATGGCAGCTCTA\n-+\n-gggggggcfcea\n-@HWI-EAS440_0386:1:25:10090:3050#0/1\n-CTGAGATACGCG\n-+\n-ghhhghhhghhh\n-@HWI-EAS440_0386:1:25:3139:3077#0/1\n-AGCTGACTAGTC\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:25:9110:3081#0/1\n-AGTGCGATGCGT\n-+\n-hhhhhhghhhhh\n-@HWI-EAS440_0386:1:25:17734:3100#0/1\n-ACTACGTGTGGT\n-+\n-ggggggggggfc\n-@HWI-EAS440_0386:1:25:8423:3141#0/1\n-ACACACTATGGC\n-+\n-hhhhhhhhhghh\n-@HWI-EAS440_0386:1:25:14009:3149#0/1\n-AGCTGACTAGTC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:3100:3158#0/1\n-CCGACTGAGATG\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:4738:3152#0/1\n-AGTGCGATGCGT\n-+\n-ggggggggggfg\n-@HWI-EAS440_0386:1:25:4197:3165#0/1\n-CGAGAGTTACGC\n-+\n-hhhhehhhhhhh\n-@HWI-EAS440_0386:1:25:9072:3171#0/1\n-CCGACTGAGATG\n-+\n-gggg_ffdffgg\n-@HWI-EAS440_0386:1:25:15751:3166#0/1\n-AGTGCGATGCGT\n-+\n-fcccffdfffgg\n-@HWI-EAS440_0386:1:25:3473:3225#0/1\n-CTGAGATACGCG\n-+\n-gfgfggfggggf\n-@HWI-EAS440_0386:1:25:4755:3229#0/1\n-CTGAGATACGCG\n-+\n-hhhhghhhhghh\n-@HWI-EAS440_0386:1:25:3032:3237#0/1\n-CCTCTCGTGATC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:1630:3249#0/1\n-CTGAGATACGCG\n-+\n-hhhhhghhhhhh\n-@HWI-EAS440_0386:1:25:4476:3251#0/1\n-AGCTGACTAGTC\n-+\n-hghhhhhhhhhh\n-@HWI-EAS440_0386:1:25:3312:3259#0/1\n-ACTACGTGTGGT\n-+\n-hhhhhhhhghhe\n-@HWI-EAS440_0386:1:25:3550:3291#0/1\n-ACACACTATGGC\n-+\n-hhhhhhhhghhg\n-@HWI-EAS440_0386:1:25:5478:3298#0/1\n-CCGACTGAGATG\n-+\n-hhhhhhhhhfhh\n-@HWI-EAS440_0386:1:25:15346:3296#0/1\n-CCTCTCGTGATC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:3468:3322#0/1\n-ACTACGTGTGGT\n-+\n-fhdfhhhhgdfe\n-@HWI-EAS440_0386:1:25:4199:3321#0/1\n-CCTCTCGTGATC\n-+\n-hhhhhhghhhhh\n-@HWI-EAS440_0386:1:25:8568:3330#0/1\n-ATGGCAGCTCTA\n-+\n-gggggggf_fdd\n-@HWI-EAS440_0386:1:25:12050:3335#0/1\n-ACACACTATGGC\n-+\n-gggggggggggg\n-@HWI-EAS440_0386:1:25:19075:3342#0/1\n-CAGTACGATCTT\n-+\n-hfhfehgghhhh\n-@HWI-EAS440_0386:1:25:4994:3354#0/1\n-ATGGCAGCTCTA\n-+\n-gggggggffef[\n-@HWI-EAS440_0386:1:25:12091:3381#0/1\n-ATGGCAGCTCTA\n-+\n-ffffffffcaa_\n-@HWI-EAS440_0386:1:25:8594:3395#0/1\n-AGTGCGATGCGT\n-+\n-hhhhhhhhhhhf\n-@HWI-EAS440_0386:1:25:2052:3400#0/1\n-CCTCTCGTGATC\n-+\n-ggggggggfgfg\n-@HWI-EAS440_0386:1:25:11776:3405#0/1\n-ACTACGTGTGGT\n-+\n-hhhhfhhfhe[f\n-@HWI-EAS440_0386:1:25:4155:3413#0/1\n-AGTGCGATGCGT\n-+\n-fffffggggggg\n-@HWI-EAS440_0386:1:25:11052:3431#0/1\n-ACTACGTGTGGT\n-+\n-hhhhhhghhhhe\n-@HWI-EAS440_0386:1:25:4122:3435#0/1\n-ATGGCAGCTCTA\n-+\n-c_cYc`WKZP\\Y\n-@HWI-EAS440_0386:1:25:9796:3444#0/1\n-AGTGCGATGCGT\n-+\n-hhhchhhhhhhh\n-@HWI-EAS440_0386:1:25:2235:3462#0/1\n-AGCTGACTAGTC\n-+\n-fcaffffcfcgg\n-@HWI-EAS440_0386:1:25:14529:3458#0/1\n-CCGACTGAGATG\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:6708:3509#0/1\n-ACACACTATGGC\n-+\n-ffffdfffffcf\n-@HWI-EAS440_0386:1:25:13919:3507#0/1\n-CCTCTCGTGATC\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:10705:3535#0/1\n-ACACACTATGGC\n-+\n-hhhfhhghgfgh\n-@HWI-EAS440_0386:1:25:7788:3570#0/1\n-CTGAGATACGCG\n-+\n-hhaghghhhdhh\n-@HWI-EAS440_0386:1:25:2273:3577#0/1\n-ACTACGTGTGGT\n-+\n-ffffffdfffe_\n-@HWI-EAS440_0386:1:25:14850:3657#0/1\n-CCGACTGAGATG\n-+\n-aaYc^aaYZZYT\n-@HWI-EAS440_0386:1:25:11581:3662#0/1\n-ACTACGTGTGGT\n-+\n-hhhhhhhhhhhg\n-@HWI-EAS440_0386:1:25:16965:3660#0/1\n-ACTACGTGTGGT\n-+\n-hhhhhhhhhhhg\n-@HWI-EAS440_0386:1:25:8197:3691#0/1\n-CTGAGATACGCG\n-+\n-hhhhhhhhhhhh\n-@HWI-EAS440_0386:1:25:11617:3701#0/1\n-AGCTGACTAGTC\n-+\n-`\\__\\W\\\\\\Y\\^\n-@HWI-EAS440_0386:1:25:15484:3705#0/1\n-CCGACTGAGATG\n-+\n-hhhhhhhhhhhh\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/demultiplexed_sequences.fastq
--- a/test-data/split_libraries_fastq/demultiplexed_sequences.fastq Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,344 +0,0 @@\n-@L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGACATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATA\n-+\n-ACCCGGGG@G?GGGGGGGGDGGGGGGGGGGGGGGGGDGGBGGGBGGGGGGGDGEGGDDG@GGGGEEEGGGGGG388GD>DDGGEE@DDDDB>FDGD>@-:74=;A*74====?BBD@\n-@L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTG\n-+\n-GGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHBHHECCHBDHFEHAE@@BDB=B@@A2D(5553DAAAAE@EEA>;)9;==A>7B@=@78;:82?C<><9?<>>>98=@\n-@L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTA\n-+\n-IIIGIIIIGIIIIIGIIHIDIHIHHF@IIFIIIIIGIIIHIHGHBIIIGHHGIFEEEFHHHDEEDG>DBEFBDB@BB=EEBBBEGEDDBA>D@@@@BCBB;BD@@>:@@>B@?=1@@@3<9767=6>;;?\n-@L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAG\n-+\n-IIIIIGIIIIIIIGIIIIIIIIIIIFIIGEGGDIIIIIFFHIIGDGEGD>GDGIIEIGIIFH>GBDDGFGGEGBB2DBDDGBDEBEBB8?<B>B>A@D=38=AC>?>@@?DD@>=?=478;+;BE8>B\n-@L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTG\n-+\n-IIIIIHIIIIIIHEEIIEIIIIIIGGHIHEIIHDFCIGHHHCEDBIEIEEHBBEBBEIHGGGGGDHGGEEGDG?<2A5DBBBBEBEBBB@BEDEBBBE;@@@B@@8:@B@@@@AE@@A0@>=<9:;9=7>:;==<?\n-@L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAG\n-+\n-HHHGGEGEGGGGGHHHHHHHGHHGGCGGHFHHHHHHHHEDBGGHFHHHHFHHHHHFHHHHHEBFCEEDFFFDE=;@C=CCCAABBD@@:=;?=BB@>DBD=@DBBB=D6'=;;A=?=99=9.9.2,/2===79@@6@\n-@L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGT\n-+\n-IIIIIIIIGIIIDGIIIFIIHIIIIIIIIIIIIIIEIFGFGGGHIIGIIIHBHIHGIGIHI@EG@EGFFIFEDFBC<FEC@B+@BBBB82==?BB@<BB@BB)AA@8=@?@@5?<>=;;2?-?=A?\n-@L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIBIIIGIIIIIIIIIIFIIIIIIIIIIIHGIIIIIIIEDGFGEDDGDBG:@@ECGEFEBHBHFHBB@@GGBBBDBECBBGECBECBFEBDEBEBB@@2B4?<=?;A??A@A+>?\n-@L1S281_8 HWI-EAS440_0386:1:25:7669:2080#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCGACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAG\n-+\n-IIIIIIIIIIIIHGGIIHIIIIIIIHIIIHIIIIIGIHHIIIIHDIIIHHHDIIIHIIHDHGEHEHGDGHEDGDHEEFEHG,EDCDCF@EBBECB@@B6>@A@ECBBCBBEEA>BBB@@DBAB=@8@@\n-@L1S140_9 HWI-EAS440_0386:1:25:3922:2110#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTT\n-+\n-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHGHHHHGBHHHHHHHHHFHHHHEHHHHEFEHFGGFGAA>C=GGDBDEDEEBCBBEEBB>BD@BB@DBBBB=C>BCCB>EBB8?\n-@L1S105_10 HWI-EAS440_0386:1:25:3806:2202#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAG\n-+\n-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGBGGGEGGGG@GGDGHHFGHHHHHHGGFEGBGGG3CE>EAABGDBFFEDFE>E>DCB@EFFBC>EDBDD+CAA>>9?=99DCC?A"..b'GCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTGAGGCTAGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIHIHIIGIIGIIHIIIIIIHHIBIIIIIIIGIEIHGIIIEHII@IGIHFDHIGDIHHFEEIGBB<DDFFFFEFDEBBDGGBFCEECDDD@D@FBBDD;BBAA@D9D::?3=<65855;:<\n-@L1S8_76 HWI-EAS440_0386:1:25:2235:3462#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAGTCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCA\n-+\n-HHHGEGGGFGBGGHHHHHHFCHHHHHHHHHHHHHHDHEFFFG@EEEF<HFHHHHDHF8DHBHHHAGHGFFDADDDFCBEEDDACEBEBEB7>E>>)>@EDCC@B<>:5:6:>68>0A;9>;:@?<>??@B\n-@L1S57_77 HWI-EAS440_0386:1:25:6708:3509#0/1 orig_bc=ACACACTATGGC new_bc=ACACACTATGGC bc_diffs=0\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAG\n-+\n-GGGHHHHHHHGHHHHHHHHGHHHHHGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGBHHHHHBHHHHHHHFHGHBHHFGEGEEBEHHHDDDB@GB=?=?EEE>EBD3=@AABDDD>BBCA<A=A\n-@L1S281_78 HWI-EAS440_0386:1:25:13919:3507#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGG\n-+\n-IIIIIHIIFIIIGGHIIHIDIHIIGBIIIEIIIHHEIIHEGHHHEHGIDBEGBIFEFFEEHEBHEFCHGGHEHE@BHBFDFEEGEDDEBBBHE@DBBDBEBBEDEEDBE>AECDCDB@BB@:C@BB@B=0=0>?=>@\n-@L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n-+\n-IIIIIIIHIIIIHIIIIIIIIIIIIIIIIIIIIHIIIIIIHIFIIIIIHHIFIIIHGHHIHIIIHHIIFFICIB8BDGD@DBACFEDGCEEBFFFCBBBEBEBAA;8?>?AAABBCC@BB>>C@DB@B@7@@@83;8@89<7+=8=(=5?9?\n-@L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTG\n-+\n-<@@GGGGGGGBGGGGGGGGGGGGGGGGGGGGDEGGGGGGGGGGGBGGGGGGDGGGB<BGGGGGGGGGG><GGGDGDGGGEGDGGGGGEGFE<DGDDDDGGGBGDDGD:BBDDD??:<?GGDBB;B\n-@L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGG\n-+\n-IIIGIIIIGHIIGGIIIIIHIIIIHIHIIIHIIIIEIEIFFGGGIFIHIIHFIHIHDFIIIGEHEHHIHIGGFEGG<HEGBD>@>ADAEEE@D?A=<=@B@@@B@B>BBBBCA@@)>@<4>1>@@>;>A4:@A\n-@L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAG\n-+\n-IIIIIIIIIIIIIIIIIIIHIIIIIDIIIIIIIIIHIIHIIIIIHIIIHDIFIIIIIIIIIIHIGIGIHHIEIFFEIEIHIFIGGHGHDHHHGHGB<EEDHEFGGHBGEDHHHBCBEBEED@B8@@@A@B@@@8?3?\n-@L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCG\n-+\n-IIIIIIIIIIIIHIIIIIIIIIIIHGIIIHIIIIIIIIIHHIIIIIGFIIIIIIIIIIIIIHGIFFGIFIIFIGHBIHGIHIGHGGEDDBDBFD>B@@BBB=BBDB?@B:BBBEEECB??A4@4?==?\n-@L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAG\n-+\n-=B@GDGGGEGEGGGGGGGGEGGGGGDGGGGEEEGGGBGGGGGGGDGGGGGGG@EEBBE???DBGGGEGBGGDGGGGBC?0?<BFGF>BDGDDGCBDDDDDDDDEGGFDDDAG+(2:39DBAAA\n-@L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGG\n-+\n-IIIIIIIIHIIIIIIIIIIGIIIIFFIIIFIIIIIHIIIHEIIIHIIIHHIFIIIIHIIIHHHIGHHFHIHEIDBBFGHFHFEHEIIEBDBEEDCDEF=DBDDCBD=D@BDEBDFCC>B@B4B=@=>@=BB>8?\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/forward_reads.fastq
--- a/test-data/split_libraries_fastq/forward_reads.fastq Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1000 +0,0 @@\n-@HWI-EAS440_0386:1:23:17547:1423#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGGGGGGATTGGTGTG\n-+\n-hhhdHddddddddfehhfhhhghggfhhhfhhgggfhhgfgdfcfhehfdgfhggfggfggffgddfgdffdgdaagaaddcbdccc]a^ad__a]_____ba_`a`__^__\\]^OWZR\\Z\\\\WYTZ_U^BBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:14818:1533#0/1\n-CCCCNCAGCGGCAAAAATTAAAATTTTTACCGCTTCGGCGTTATAGCCTCACACTCAATCTTTTATCACGAAGTCATGATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGGCACATTAAATTTAAACTGATGATTCCACTGCAACAA\n-+\n-US[QCQSZPHNYIa[^aaccaac[]accBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:14401:1629#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGGGGTTGGGGG\n-+\n-fffbF`bbWZZ]Zggggfgcgggggddggdgggggdbgdddgbgeggg`ffdggeabba`aaad]]]d\\]`]`[]]aWaYa\\aa`a`_````_^]^^^]]]X]_``____``BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:15259:1649#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGAGTTTGGGGG\n-+\n-hhhdHcdd^bbbahhhhhhfhhhhhghhhhhhhhhghhhgehchfhhhgghghfhhhgehgaffaecfdggdh\\bafadddddgddfdbc^]a_\\^_a``\\X`^_`]`aaabcaYbY_^^X]^ZY^Z^a`_^aBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:13748:2482#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGGATTCGTGGTG\n-+\n-fffbF^bbS[T[Uggggggg__gffddfggeggggaagfeefbfaaff_cfacfeceddgggegdgdgaggddcddd`a_aad`ddadd`daaWY]]Yddda_]_]]a_Y___X\\_]YaY]\\]WYNV]\\]_BBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:6532:3028#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGAGTCTTGGGG\n-+\n-hhhfHdffacdcchhhhghfhhhhfehhhchhhehghhgghhgehghhffghhhgghghddgggfhfgdhhdea`Wf^dddddbgagcdedgcfddbcddaddcefb_addddd_daaaaaaa`ca`aX^Z\\X_^^^^BBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:8677:3027#0/1\n-TACANAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGCCGGCACATGATACTGTGAGACTAGCGTAACGGAGGGGGAACCGGAATTCTTGGTG\n-+\n-ggg`Fbbbdeeeegggggggggggfgggggggggggggggggfgggggggggfgggggggf]gfccfcfbfbdged]ddda_dedaa]aZc__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:5678:3052#0/1\n-TACGNAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAAGAGCAAGTCTGATGTGAAAGGCTGGGGCTTAACCCCAGGACTGCATTGGAAACTGTTTTTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTGGGG\n-+\n-hhheHeeeaaabbhghhhhhhhhhghhhhghhhhhfhghhghhghhhhdhehhfghhaehhgghddhhhhhadffffdb]Z__Z^_`^daadda`c`Z\\T[\\\\]\\RJ]YS[\\X_a]]P_XM\\T\\^\\^^BBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:11889:3171#0/1\n-TACGNAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTATGACTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTG\n-+\n-hhheHddeeeeddhghhhhhhhhhhchhhhhhhhhfhfdddffhgghhghgehhegghhhhffhffhhg_edaecdcc[dabaadddaadaaeY\\WQX^]]^^``RZZ___a__aa_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:2112:3374#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGGGGGATTCGTGTGG\n-+\n-fffdGcddZZ___ggggggggggggggggfggggggfgdggggeggggeggggggeggdggeggggggdggdgcaaf\\^_b_b_gdedd_eedR^Z^^`dcRb_P__R^\\[]^c`cbadaaab^da^aBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:5900:3393#0/1\n-TACGNATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGAAGGCTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGGTCATCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTG\n-+\n-hhheHeeea\\aaaghhhhhhhhhhhhhhhhghhhhfhgggghhhhhhfcghhhhgfhdgahddfbddfcfca]daed]cfcdcb]bbb^]_^bUZRYW___^_abaV_^SYYW````]^_[O_^```Z\\RS^BBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:23:15468:3455#0/1\n-TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGA'..b'TCGGTG\n-+\n-hhhhhhhhghhhghhhhhhegfhhfhfhahghhhchhdhhhhahhhhhggchffgggghhggfhbefbfbd_dddcdaR`_`a_NU^^^^__^`^`G^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:6708:3509#0/1\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTG\n-+\n-fffgggggggfggggggggfgggggfggggggggggggggggfgggggggggggfagggggagggggggegfgaggefdfddadgggccca_fa\\^\\^ddd]dacR\\_``accc]aab`[`\\`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:13919:3507#0/1\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGGATTCGTGGGG\n-+\n-hhhhhghhehhhffghhghchghhfahhhdhhhggdhhgdfgggdgfhcadfahedeeddgdagdebgffgdgd_agaeceddfdccdaaagd_caacadaadcddcad]`dbcbca_aa_Yb_aa_a\\O\\O]^\\]_BBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:10705:3535#0/1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAACTGGCCGGCTAGGGTGTCCGGGGGGGACAGGGGATTTCCTGTGT\n-+\n-hhhhhhhhdhhhhhhhhhhhhhhhhehhhhhhhffdfeffffchhhhhhghhhhhhhhfhhhfhdhchhfheagghhcahgeg_ddbadeedh`][^`Z_ZZ```RK^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:7788:3570#0/1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n-+\n-hhhhhhhghhhhghhhhhhhhhhhhhhhhhhhhghhhhhhghehhhhhgghehhhgfgghghhhgghheehbhaWacfc_ca`bedcfbddaeeebaaadada``ZW^]^```aabb_aa]]b_ca_a_V___WRZW_WX[VJ\\W\\G\\T^X^\n-@HWI-EAS440_0386:1:25:2273:3577#0/1\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGACTTCCCGGTG\n-+\n-cfffeffeggaggffffdggdgggggaggggggee]fb`]```fcfgdgaffgffbbd[ca_W]Z``ZY^]U]YS[^`_`_`\\`add```aa]a_[[a`a_a```a`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:14850:3657#0/1\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTGTGGTTGAGGTAGGCGGAATGCGTGGTG\n-+\n-[__fffffffaffffffffffffffffffffcdfffffffffffaffffffcfffa[affffffffff][fffcfcfffdfcfffffdfed[cfccccfffafccfcYaaccc^^Y[^ffcaaZaBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:11581:3662#0/1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGGGTAAGCGGAATTCCTAGGG\n-+\n-hhhfhhhhfghhffhhhhhghhhhghghhhghhhhdhdheefffhehghhgehghgcehhhfdgdgghghffedff[gdfac]_]`c`ddd_c^`\\[\\_a___a_a]aaaab`__H]_[S]P]__]Z]`SY_`BBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:16965:3660#0/1\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGGGGGATTTGTGGGG\n-+\n-hhhhhhhhhhhhhhhhhhhghhhhhchhhhhhhhhghhghhhhhghhhgchehhhhhhhhhhghfhfhgghdheedhdhghehffgfgcgggfgfa[ddcgdeffgafdcgggabadaddc_aW___`_a___W^R^BBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:8197:3691#0/1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGCG\n-+\n-hhhhhhhhhhhhghhhhhhhhhhhgfhhhghhhhhhhhhgghhhhhfehhhhhhhhhhhhhgfheefhehhehfgahgfhghfgffdccacaec]a__aaa\\aaca^_aYaaadddba^^`S_S^\\\\^BBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:11617:3701#0/1\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTG\n-+\n-\\a_fcfffdfdffffffffdfffffcffffdddfffafffffffcfffffff_ddaad^^^cafffdfaffcffffab^O^[aefe]acfccfbaccccccccdffeccc`fJGQYRXca```BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n-@HWI-EAS440_0386:1:25:15484:3705#0/1\n-TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGGTAGGCGGAATGGATGGTG\n-+\n-hhhhhhhhghhhhhhhhhhfhhhheehhhehhhhhghhhgdhhhghhhgghehhhhghhhggghfggeghgdhcaaefgegedgdhhdacaddcbcde\\caccbac\\c_acdacebb]a_aSa\\_\\]_\\aa]W^BBBBBBBBBBBBBBBBBB\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/histograms.tabular
--- a/test-data/split_libraries_fastq/histograms.tabular Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-Length Count
-116.0 20
-126.0 31
-136.0 33
-146.0 2
-156.0 0
---
-

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/histograms.txt
--- a/test-data/split_libraries_fastq/histograms.txt Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-Length Count
-116.0 20
-126.0 31
-136.0 33
-146.0 2
-156.0 0
---
-

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane1_barcode.fastq.gz

Binary file test-data/split_libraries_fastq/lane1_barcode.fastq.gz has changed

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane1_read1.fastq.gz

Binary file test-data/split_libraries_fastq/lane1_read1.fastq.gz has changed

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane2_barcode.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/lane2_barcode.fastq Sat Aug 05 07:33:48 2017 -0400

b'@@ -0,0 +1,1000 @@\n+@M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@@FFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:17088:1773 1:N:0:0\n+CACTCAACAGAC\n++\n+C@@FFFEFBFHH\n+@M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0\n+CTCGCTTCACTT\n++\n+B@@DFFFF<FFH\n+@M00176:17:000000000-A0CNA:1:1:12561:1773 1:N:0:0\n+GCGTGCTGGGAT\n++\n+::+<<)?ABCAB\n+@M00176:17:000000000-A0CNA:1:1:14596:1773 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@FFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:12515:1774 1:N:0:0\n+GTCCGCTGAATA\n++\n+1+1+2)<A8AC<\n+@M00176:17:000000000-A0CNA:1:1:17491:1774 1:N:0:0\n+ATTGCGGCGGCG\n++\n+79(((0-(-(0(\n+@M00176:17:000000000-A0CNA:1:1:16427:1774 1:N:0:0\n+GAGTAGCTCGTG\n++\n+B=?DDEFDHHHB\n+@M00176:17:000000000-A0CNA:1:1:13372:1775 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@@FFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:14806:1775 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@?DDFFFHGHG\n+@M00176:17:000000000-A0CNA:1:1:13533:1775 1:N:0:0\n+CGGCGCAAGATT\n++\n+=?;A4<@1CFHH\n+@M00176:17:000000000-A0CNA:1:1:18209:1775 1:N:0:0\n+GTTGTAGTGGAG\n++\n+--7(()2))(2(\n+@M00176:17:000000000-A0CNA:1:1:16020:1776 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@@FFFFFHHGH\n+@M00176:17:000000000-A0CNA:1:1:12460:1777 1:N:0:0\n+ACTTGCCCTCAC\n++\n+?@@DDBDDHHHH\n+@M00176:17:000000000-A0CNA:1:1:17898:1778 1:N:0:0\n+TTCACCATAGGT\n++\n+@@@DD?BD??FH\n+@M00176:17:000000000-A0CNA:1:1:12607:1778 1:N:0:0\n+CATGTGGTGGGA\n++\n+0(((()22:<8(\n+@M00176:17:000000000-A0CNA:1:1:16637:1778 1:N:0:0\n+ACTGGTTGAGTC\n++\n+BB@DDDEFFDFF\n+@M00176:17:000000000-A0CNA:1:1:12658:1778 1:N:0:0\n+AGAGTAGCTAAG\n++\n+B@8BDBDDHHHF\n+@M00176:17:000000000-A0CNA:1:1:14889:1778 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@FFFDFHHHH\n+@M00176:17:000000000-A0CNA:1:1:14503:1778 1:N:0:0\n+ATTGTCGGTGTA\n++\n+=?@AD?DDHHHF\n+@M00176:17:000000000-A0CNA:1:1:15599:1778 1:N:0:0\n+TTAGGCATCTCG\n++\n+@@@FFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:16864:1779 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@FFFFFHHHG\n+@M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0\n+ATCTCCTCTCCA\n++\n+@BBFFFDEFHDF\n+@M00176:17:000000000-A0CNA:1:1:18258:1779 1:N:0:0\n+TGCCATCTGAAT\n++\n+@@@D1DDDHHF?\n+@M00176:17:000000000-A0CNA:1:1:13050:1779 1:N:0:0\n+TACGACTTTAGC\n++\n+@BBDDDDFHHHH\n+@M00176:17:000000000-A0CNA:1:1:16097:1779 1:N:0:0\n+GGTTCACCATAG\n++\n+??:BDADFCBHF\n+@M00176:17:000000000-A0CNA:1:1:12253:1779 1:N:0:0\n+TTAGGCATCTCG\n++\n+B?@DFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:13138:1780 1:N:0:0\n+CGTTTCCGTTTC\n++\n+@@BFFDDFHDFH\n+@M00176:17:000000000-A0CNA:1:1:14840:1780 1:N:0:0\n+GGAAGCTTGTCT\n++\n+=?1ABBDDHF?F\n+@M00176:17:000000000-A0CNA:1:1:17206:1780 1:N:0:0\n+GGAGTTTCCACA\n++\n+B@:DDEFFFHHD\n+@M00176:17:000000000-A0CNA:1:1:17334:1781 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBCFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:17037:1781 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBBFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:16198:1781 1:N:0:0\n+GTAACCGTAACC\n++\n+=11ABA?DDFCF\n+@M00176:17:000000000-A0CNA:1:1:14924:1781 1:N:0:0\n+ATTACGGCGGCC\n++\n+=@@A:B)8DF0)\n+@M00176:17:000000000-A0CNA:1:1:17275:1782 1:N:0:0\n+TTAGGCATCTCG\n++\n+@??DDDFFHGH?\n+@M00176:17:000000000-A0CNA:1:1:16914:1782 1:N:0:0\n+CTGTAGGTTAAT\n++\n+1+12+2+2+2+2\n+@M00176:17:000000000-A0CNA:1:1:15172:1782 1:N:0:0\n+GAACTGTATCTC\n++\n+B?=DFFD,CFHF\n+@M00176:17:000000000-A0CNA:1:1:13951:1782 1:N:0:0\n+TTAGGCATCTCG\n++\n+@@@DFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:17573:1783 1:N:0:0\n+CTTCTAAGGAGC\n++\n+B@BDFFDDHHHH\n+@M00176:17:000000000-A0CNA:1:1:18622:1783 1:N:0:0\n+TTTTGCATCTCT\n++\n+==+<1+)24).)\n+@M00176:17:000000000-A0CNA:1:1:13264:1784 1:N:0:0\n+TTAGGCATCTCG\n++\n+@@?DF;DDHBBF\n+@M00176:17:000000000-A0CNA:1:1:19051:1784 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBCFFFFFFHGH\n+@M00176:17:000000000-A0CNA:1:1:18234:1785 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBBDFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:18726:1785 1:N:0:0\n+TTAGGCATCTCG\n++\n+@@@FFFFFHHGG\n+@M00176:17:000000000-A0CNA:1:1:12958:1785 1:N:0:0\n+ATTCAGCACCAG\n++\n+B@@FDFF8DHHF\n+@M00176:17:000000000-A0CNA:1:1:18601:1785 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@DFFFFHHGG\n+@M00176:17:000000000-A0CNA:1:1:18699:1785 1:N:0:0\n+GTGGACGTCCAA\n++\n+=:+BBBD?@BDB\n+@M00176:17:000000000-A0CNA:1:1:18674:1786 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@@DFFFFHHHB\n+@M00176:17:000000000-A0CNA:1:1:12910:1786 1'..b'00-A0CNA:1:1:14447:1833 1:N:0:0\n+CTAATTACACGC\n++\n+BB?DFFFFAHHH\n+@M00176:17:000000000-A0CNA:1:1:12871:1833 1:N:0:0\n+GAGTCGCGTTTA\n++\n+:::4=@DDFHHG\n+@M00176:17:000000000-A0CNA:1:1:18056:1834 1:N:0:0\n+CATGAGTGCTAC\n++\n+BBBDDFDEHHHH\n+@M00176:17:000000000-A0CNA:1:1:17984:1834 1:N:0:0\n+TTAGGCATCTCG\n++\n+=?7B?DFDHHHG\n+@M00176:17:000000000-A0CNA:1:1:15416:1834 1:N:0:0\n+ATCTCACCGTAA\n++\n++11++,2+@22)\n+@M00176:17:000000000-A0CNA:1:1:15709:1834 1:N:0:0\n+CGAATGACGCCA\n++\n+?@?DDFFDFHF>\n+@M00176:17:000000000-A0CNA:1:1:15154:1834 1:N:0:0\n+TTAGGCATCTCG\n++\n+CCCFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:13838:1834 1:N:0:0\n+ATTGCCCCGATG\n++\n+?@@DBDD+@8CF\n+@M00176:17:000000000-A0CNA:1:1:16996:1835 1:N:0:0\n+AGGTCTAGGGTC\n++\n+=@@+=ADD>=CD\n+@M00176:17:000000000-A0CNA:1:1:15945:1836 1:N:0:0\n+GACTCAGCAACA\n++\n+B?@DDD3BAFFD\n+@M00176:17:000000000-A0CNA:1:1:15829:1836 1:N:0:0\n+GTGAACTTGGGC\n++\n+B:?DDDEFHGHH\n+@M00176:17:000000000-A0CNA:1:1:18386:1836 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB?DFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:12988:1836 1:N:0:0\n+GTGGACGTCCAA\n++\n+=:=A==@DHHHD\n+@M00176:17:000000000-A0CNA:1:1:15728:1836 1:N:0:0\n+TTAGGCATCTCG\n++\n+@CCFFFFDHGHH\n+@M00176:17:000000000-A0CNA:1:1:13129:1837 1:N:0:0\n+GTTTGGCGACGA\n++\n+=1=BBDDDFHHH\n+@M00176:17:000000000-A0CNA:1:1:18507:1837 1:N:0:0\n+CCACACCTTCTG\n++\n+BBBDDDDDHHHF\n+@M00176:17:000000000-A0CNA:1:1:14782:1837 1:N:0:0\n+GATTTTTCTATG\n++\n+++1++,2+))))\n+@M00176:17:000000000-A0CNA:1:1:15801:1837 1:N:0:0\n+AGTACTGCAGGC\n++\n+<@BDDFBDBFHH\n+@M00176:17:000000000-A0CNA:1:1:16705:1837 1:N:0:0\n+GCACTCGTTAGA\n++\n+B@<DDDDEFHHH\n+@M00176:17:000000000-A0CNA:1:1:13088:1837 1:N:0:0\n+GCTATGGACCGA\n++\n+@@@FFFF;FHHG\n+@M00176:17:000000000-A0CNA:1:1:17186:1837 1:N:0:0\n+GTTAAGCCCGAT\n++\n+:1=1=A?+C:A:\n+@M00176:17:000000000-A0CNA:1:1:17204:1838 1:N:0:0\n+CATCGTATCAAC\n++\n+B@BFDDEFGHHH\n+@M00176:17:000000000-A0CNA:1:1:16197:1838 1:N:0:0\n+AGTACTGCAGGC\n++\n+@BCFFFDEBFHH\n+@M00176:17:000000000-A0CNA:1:1:14193:1838 1:N:0:0\n+TCTTATCCCCAT\n++\n+1++2<7+222++\n+@M00176:17:000000000-A0CNA:1:1:12840:1838 1:N:0:0\n+CGAGTCTAGTTG\n++\n+=B:BDBB=CCFD\n+@M00176:17:000000000-A0CNA:1:1:17335:1838 1:N:0:0\n+TTAGGCATCTCG\n++\n+BCCFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:12956:1839 1:N:0:0\n+GATCCACGGACA\n++\n+B?BDFDDDHFFH\n+@M00176:17:000000000-A0CNA:1:1:18356:1839 1:N:0:0\n+GCAGCCGAGTAT\n++\n+B@BDDDADHHHH\n+@M00176:17:000000000-A0CNA:1:1:19008:1839 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@FFFFFHHHF\n+@M00176:17:000000000-A0CNA:1:1:17738:1839 1:N:0:0\n+ACGTGGTTTCGT\n++\n+BBBBDDDFHHGF\n+@M00176:17:000000000-A0CNA:1:1:12224:1840 1:N:0:0\n+NAGGGAGGAGAC\n++\n+#1144=@DDBHF\n+@M00176:17:000000000-A0CNA:1:1:14532:1840 1:N:0:0\n+GATCAACTACCG\n++\n+?8?DDDDD?FC@\n+@M00176:17:000000000-A0CNA:1:1:13369:1840 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBBFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:17458:1840 1:N:0:0\n+GGACAACGCTTG\n++\n+=::ADDFF?FFF\n+@M00176:17:000000000-A0CNA:1:1:12385:1841 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@DDFFFHHHG\n+@M00176:17:000000000-A0CNA:1:1:14003:1841 1:N:0:0\n+GATCAACTACCG\n++\n+@=@DFDDDFHF?\n+@M00176:17:000000000-A0CNA:1:1:16682:1842 1:N:0:0\n+TTAGGCATCTCG\n++\n+CCCFFFFFHHHG\n+@M00176:17:000000000-A0CNA:1:1:14923:1843 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBCFFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:12467:1843 1:N:0:0\n+AGTATTTATATG\n++\n+((-(-9..)@)=\n+@M00176:17:000000000-A0CNA:1:1:16919:1843 1:N:0:0\n+TTAGGCATCTCG\n++\n+8:?DADD?;:D:\n+@M00176:17:000000000-A0CNA:1:1:17484:1844 1:N:0:0\n+GACCAAAGTGGA\n++\n+18;DAD+A,+<@\n+@M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0\n+AGGGTTCCAGTT\n++\n+?@BDDEBE8BFD\n+@M00176:17:000000000-A0CNA:1:1:16762:1844 1:N:0:0\n+TTAGGCATCTCG\n++\n+@B@DFFFFHHHH\n+@M00176:17:000000000-A0CNA:1:1:16590:1845 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@DDFDFDDHH\n+@M00176:17:000000000-A0CNA:1:1:14102:1846 1:N:0:0\n+CCAGTAGTCTTA\n++\n+BB=BDDAEHHHD\n+@M00176:17:000000000-A0CNA:1:1:13058:1846 1:N:0:0\n+TTAGGCATCTCG\n++\n+BB@FFFFFHHGH\n+@M00176:17:000000000-A0CNA:1:1:12794:1846 1:N:0:0\n+TTAGGCATCTCG\n++\n+B@@FFFFFHHGH\n+@M00176:17:000000000-A0CNA:1:1:15066:1846 1:N:0:0\n+TTAGGCATCTCG\n++\n+BBCFFFDFHHHH\n+@M00176:17:000000000-A0CNA:1:1:15485:1847 1:N:0:0\n+TTAGGCATCTCG\n++\n+=?=AAD;B?DFF\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane2_barcode.fastq.gz

Binary file test-data/split_libraries_fastq/lane2_barcode.fastq.gz has changed

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane2_read1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/lane2_read1.fastq Sat Aug 05 07:33:48 2017 -0400

b"@@ -0,0 +1,1000 @@\n+@M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0\n+GCTTAGGGATTTTATTGTTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTCATGAACTTAATCCACTGTTCACCATAAACGTGACGATGAGG\n++\n+C@CFFFFFHHFHHGIJJ?FFHEIIIIHGEIIFHGIIJHGIGBGB?DHIIJJJJCFCHIEGIGGHGFAEDCEDBCCEEA.;>?BB=288A?AB709@:3:A:C88CCD@CC444@>>34>>ACC:?CCD<CDCA>A@A>:<?B@?<((2(>?\n+@M00176:17:000000000-A0CNA:1:1:17088:1773 1:N:0:0\n+AACATAGGTCACGAGCATTATCCGGATTTATTGGGCGTAAAGGAAGCGTAGGCGGGGAGGTTGATCCATTGTTAAAAGCATTTGCTTAACAAATGTGTGCATTGGAGATCGCCTCCCTAGAGTTAATCAGGGGGGACTGGAATTCAATGTG\n++\n+@@CDDFFFHFBHHIIIEHIBHIIIIGIIIIIIIIIIAGHGHHIHGGGIHHIIGGF65&7-2(3(+4:44:>C@ADC>:?>:>:@:>@>CA@CB@@++:<A>C:ACACCC:<299>ABC:A3>A::>@C:>(20<.&0<AB(+:C@3:>(+:\n+@M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0\n+TACGTAGAAGACTAGTGTTAATCATCTTTATTAGGTTTAAAGGGTACCTAGACGGTAAATTAAACTCTAAATGAGTACTTGTTTACTAGAGTTTTATGAGAGAAGGAAGAATTTTGGGAGTAGTGATAATATACGTTGATCCCTGAAAGAC\n++\n+@@@DBD;;FHBHDGGIIIIIIGH@HEGGHHIII9+:*??<?BGG19?BF9F396?DGHDGF:F>FGIIII>D4)@@CCEHEEHDDE<B@7;;>>ACECC3>C?A59ACB@CACC@:5><<23(>>ABC@CADCD8AC?<>AC9:4?>:((+\n+@M00176:17:000000000-A0CNA:1:1:12561:1773 1:N:0:0\n+GACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGGGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTACCGGG\n++\n+@@CFADFFFHHHDHIIIIJIJJIIJJIIGHJJIJJGIJJJJJCGGAHHIJJJEGHH;C>DEB;ADDDA/;?@BDDDDCDDDDDDDBBDDDDDDCB12:?8?B509>3@BC4+4<CDB?4>ABBDCC?B9<9<@B9<BB?@>9<BA(+(05&\n+@M00176:17:000000000-A0CNA:1:1:14596:1773 1:N:0:0\n+CTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTT\n++\n+CCCFFFFFAHGHHJIJJJJJ>HEIJJJJJJJIGGFIJGHGGHFHJIIIIIIIHCHIDIIJJGBGGIIEEEFFDDDCEEEDDDEA@;=;@DDDADDDCECDDB?CA@CCACCDDD>@CCCACD<?>>CD@>>CBD@528<>>A??C>A?@:>\n+@M00176:17:000000000-A0CNA:1:1:12515:1774 1:N:0:0\n+GACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGGCGTAAAGGGCACGTAGGCGGTGAATCGGGTTGAAAGTGAAAGTCGCCAAAATCTGGTGGAATGCTCTCGAAACCCATTCACTTGAGTGAGACAGAGGAGTGTGGAATTTCGTGTGT\n++\n+@@@DDDDDB66B5??+>AD8A@CBBB<BCC8@CBBABBBBBCC?<<@@BCBBCBB5:?3>@?BBB?BC@:>CACECC:ABB28&9((+4@::AB<A4@:@@C(0+9<0288A@>:ACCCCCCC3::@3939?(8+2+4<3>4>A>92?(+2\n+@M00176:17:000000000-A0CNA:1:1:17491:1774 1:N:0:0\n+TACGTAGGGTCCGAGCGTTGTCCGGAGTTACTGGGCGTAAAGCGCGCGCAGGTGGCTCGATAAGACTGGCGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCGTTGGGGACTGTCGAGCTTGAGGGCAGCAGGGGCAGGGTGGATTCCCGGG\n++\n+@@@DDFFFGHHFHGGIJJIJJJGIJIJHIIIJCHIJF'5@@CHEADDD>B@?<CBDDCBDDDBDDDDCDBDD;?@CCC?BDD7@BBBCCCAB@BD99<@<?305?1&0(988:A<<@<5@9<C?8509(28?3<3<9<&(+)2>A34>9@.\n+@M00176:17:000000000-A0CNA:1:1:16427:1774 1:N:0:0\n+AACATAGGTCACGAGCATTATCCGGATTTATTGGGCGTAAAGGAAGCGTAGGCGGGGAGGTTGATCCATTGTTAAAAGCATTTGCTTAACAAATGTGTGCATTGTAGATCGCCTCCCTAGAGTTAATCAGGGGGTACTGGAATTCAATGTG\n++\n+@CCFFFFFHHGHHBHJIJJJJJJJJIJJJJJJJFIJ<6DHHHJJJGGIJIJIGHF=B6<<<AC?34>3>CACDCDDD38>:>+4>AC@C>A><((+448:>C(+4(4>4@<@>5>BD9(3:ACD>A@3(+:8@&)5>:@>9:AA::>CC((\n+@M00176:17:000000000-A0CNA:1:1:13372:1775 1:N:0:0\n+CATCAGGGTTAGGAACATTAGAGCCTTGAATGGCCGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATCGGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAATTTAGACATGGCGCC\n++\n+???DDDDDDDD3CEEEEEII3A3AEEF9EEICEE3DDDIDEIDEIIIIIIIICECDIIAE@>ADEACCDDDECD@AD@;?/>AA5=2<?AA3><AAAAA3:>4:A??9;&5<9&50;>>>5<:45>>>;?>A(8<<:>A>A:>A>((+059\n+@M00176:17:000000000-A0CNA:1:1:14806:1775 1:N:0:0\n+AACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCA\n++\n+CCCFFDDDHHHHHIIIIDHHBIIIGGHEDF+<<8?CF>BGG?9@6@GAHIGH9??GGGGGIGIIGGEBHGCEHHHFEBBBCDACCCEACCCCCDCCA@AA>C:C@CBBCCDC:@CCAACDDDC:3?<<1@CA>C>ACBD>>@<??8AC<<(\n+@M00176:17:000000000-A0CNA:1:1:13533:1775 1:N:0:0\n+TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGTAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGG\n++\n+CCCFFFFFDDHFFIJJJJJJIGIJJJEIJJIJJIJFIIJJJIII<AEFFFDDDDDDDDDBCDDDEDCDCCDECDDDCDDC85<BBDDCDDDC@DBACB@AC:@C3:AACDCDDDCC@ACACB>>CC@A+8824259@D&)<>A@(:>:>(&\n+@M00176:17:00000000"..b'CDDD>A@ABCCDDCD1>80.5.5@B<@<00)<(::??<\n+@M00176:17:000000000-A0CNA:1:1:12467:1843 1:N:0:0\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGTTGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAGACTTGGGTGCAGAGGAGGTAAGCGGAATATGTTGT\n++\n+???D=BDD=ADDDIIEIIIIIIIIII)C?D?DEII8?DDIII4A5@ADD@?A5;?805<=?=AAEEAA((:>?ADAAA<?1+5>??9AA??>+802(2&(98:::AA:3>>:>((((3>>A:2<;((4:2<<<;(:4:+5;?;?+(((+(3\n+@M00176:17:000000000-A0CNA:1:1:16919:1843 1:N:0:0\n+TCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGAATCAAGGCTCTTAAACCTG\n++\n+@?=DDDBDHF?DC9E2@CFD<?<G>9ACEAHA??9?:DD9?BGGEB8<?8BB=).=;37@=@=D<;@D;C;B>;3=@>3@ACB@35<5>;;;;:3:>(4>3>C@@AC3)29B5>>ACCDCCB3@C3(+849&0&8(4>:?@?CCCA@:9?1\n+@M00176:17:000000000-A0CNA:1:1:17484:1844 1:N:0:0\n+AACATAGGTCACGAGCATTATCCGGATTTATTGGGCGTAAAGGAAGCGTAGGCGGGGAGGTTGATCCATTGTTAAAAGCATTTGCTTAACAAATGTGTGCATTGGAGATCGCCTCCCTAGAGTTAATCAGGGGGGACTGGAATTCAATGTG\n++\n+CCCFFFFFHHHHFIJJJIJBHJIJJJIIJIIJJJJJBFHJEHIJGEHH@GIJHHFDD&5<8?334>C>AD@CDACD:>ACDCDCAAC:A>:CBCDCD@ACAAA(:4(3>:<<<5>2<?4<ACCCC@CC:@C?>>&&0<BD9AACC@@>CCD\n+@M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0\n+TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCCGGGGCTTAACTCCGGGCGTGCATGCGATACGGGCATAACTTGAGTACTGAAGGGGTAACGGGAATTCCTGG\n++\n+B?@DDFFFDFHHHIIGHIIGIJIJIIGHHHGJIGGIDIJJJIIICEHD9ACB>@BDDDDDDD?BDDB>?BBDD<@ACDD@?5&5<9<AC@CCCDB.<0099A(4350?5.2?&5<?CC344:4>4@CA@(:4>@D&5?4+0050<A@>>@?\n+@M00176:17:000000000-A0CNA:1:1:16762:1844 1:N:0:0\n+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGA\n++\n+B@BDDFFFGHHHHA<<AFHIJFJJJIJJJJDHICGH1110:BFGJJIJFIIIJJIJJJGJIIDGHIIGGHHFBHHFFFCCDDDC:>ACBCCDEEFDBDDDDEED@C<<ADDCCDDDBDDD93>ACCCCCB<9B@C:(:>@CC<BA?CDCA3\n+@M00176:17:000000000-A0CNA:1:1:16590:1845 1:N:0:0\n+GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCGGATTATTTTG\n++\n+@@=DDDDBHFFHH?2<<EEBE?FFFHHIIIGBC<FC1*11?CDGFDGGG9??DFFHHIGGHFHG@CEIIF;C=.=ACCCCE@BCC9>>CCA@CCC@CBBBCCCC0<AC>CCCBB?BBCCCC>:A?@A?CC>@AC>>C:9(&))55@AD:@4\n+@M00176:17:000000000-A0CNA:1:1:14102:1846 1:N:0:0\n+AACATAGGTCACGAGCATTATCCGGATTTATTGGGCGTAAAGGAAGCGTAGGCGGGGAGGTTGATCCATTGTTAAAAGCATTTGCTTAACAAATGTGTGCATTGGAGATCTCCTCCCTAGAGGTAATCAGGGGGGACTGGAATTCAATGGG\n++\n+CCCFFFFFHFHHHIJIHIJGIIIJIJJGJGIJIIJGIFHHGHCHIIIJEGIHHFF@B-7B8?3>ACD>AD:@@44>C@??C@CA@3A(:34@BCA:ABBD@:4(+(3+>C(:>3?>?9+3::(4>>C@CDCB@@&058<A93>>:((4:((\n+@M00176:17:000000000-A0CNA:1:1:13058:1846 1:N:0:0\n+CTTTTCCCAGCCTCAATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCT\n++\n+CCCFFFFFGHHHGJJEGIHIIIIIJIGIJJJJFGIFHIJ@GHHIJIIGHIJJIDFHJJIIIJHABCDBDDDDD<@CBBBDDDDD:>>@CDDDDDDDCCCCCDDDDDB@BC:?9@AAADDECCCDCCCCCDDDEECDEDB@9>BDD@CBB3&\n+@M00176:17:000000000-A0CNA:1:1:12794:1846 1:N:0:0\n+TCAAAAGCAATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATGCAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGACGATGTAGCTTTAGGTGTCTGTA\n++\n+B@BFFFFFHHHHGJJJJJJJIJJIIIIIIIIJIIIBGGIDFFGIHIIH9EEH>CDFFFEEEEEEDCCCCDD@CD@CDDCCDD@DDDACCCCCDDDCCCCDCABBDDDC@C<CCCDCCACEACCDCCDDCB7?@8>>CCD@CDCC>>>@CDD\n+@M00176:17:000000000-A0CNA:1:1:15066:1846 1:N:0:0\n+GAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTC\n++\n+@@@FDFFFHHHHGJJJJJJFHGGEHGIFHEGHIFGGIIJJIJJJBDHEHHJHIGBFEGFHIJCFGEGCCHHFDBBCDCCCC@CDDDDBA<B9C@CDDCA>5<@@<CC><>B>AC@C>CACC:@CA39<><C>A@<>8(>CC<4@:><BBA>\n+@M00176:17:000000000-A0CNA:1:1:15485:1847 1:N:0:0\n+CGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGATTCAGGTTA\n++\n+BBBDFFFFHHHHFGEHHGIHIJJJJGGIIE?;FHHDHFDDFGIJJHIIFHJIFFHGGIJGIFFFBCDDDDDCD>ACDCDCCCDDDD@BBC@@CDDDDD??CCC>ACEDDDCB5>>9CCDCCAC@BBB<<B<CDA8<>@@DDD(::(434>(\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/lane2_read1.fastq.gz

Binary file test-data/split_libraries_fastq/lane2_read1.fastq.gz has changed

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/map.tsv
--- a/test-data/split_libraries_fastq/map.tsv Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,35 +0,0 @@
-#SampleID BarcodeSequence LinkerPrimerSequence SampleType Year Month Day Subject ReportedAntibioticUsage DaysSinceExperimentStart Description
-L1S8 AGCTGACTAGTC GTGCCAGCMGCCGCGGTAA gut 2008 10 28 1 Yes 0 1_Fece_10_28_2008
-L1S140 ATGGCAGCTCTA GTGCCAGCMGCCGCGGTAA gut 2008 10 28 2 Yes 0 2_Fece_10_28_2008
-L1S57 ACACACTATGGC GTGCCAGCMGCCGCGGTAA gut 2009 1 20 1 No 84 1_Fece_1_20_2009
-L1S208 CTGAGATACGCG GTGCCAGCMGCCGCGGTAA gut 2009 1 20 2 No 84 2_Fece_1_20_2009
-L1S76 ACTACGTGTGGT GTGCCAGCMGCCGCGGTAA gut 2009 2 17 1 No 112 1_Fece_2_17_2009
-L1S105 AGTGCGATGCGT GTGCCAGCMGCCGCGGTAA gut 2009 3 17 1 No 140 1_Fece_3_17_2009
-L1S257 CCGACTGAGATG GTGCCAGCMGCCGCGGTAA gut 2009 3 17 2 No 140 2_Fece_3_17_2009
-L1S281 CCTCTCGTGATC GTGCCAGCMGCCGCGGTAA gut 2009 4 14 2 No 168 2_Fece_4_14_2009
-L2S240 CATATCGCAGTT GTGCCAGCMGCCGCGGTAA left palm 2008 10 28 2 Yes 0 2_L_Palm_10_28_2008
-L2S155 ACGATGCGACCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 1 No 84 1_L_Palm_1_20_2009
-L2S309 CGTGCATTATCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 2 No 84 2_L_Palm_1_20_2009
-L2S175 AGCTATCCACGA GTGCCAGCMGCCGCGGTAA left palm 2009 2 17 1 No 112 1_L_Palm_2_17_2009
-L2S204 ATGCAGCTCAGT GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 1 No 140 1_L_Palm_3_17_2009
-L2S357 CTAACGCAGTCA GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 2 No 140 2_L_Palm_3_17_2009
-L2S222 CACGTGACATGT GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 1 No 168 1_L_Palm_4_14_2009
-L2S382 CTCAATGACTCA GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 2 No 168 2_L_Palm_4_14_2009
-L3S242 ACAGTTGCGCGA GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 1 Yes 0 1_R_Palm_10_28_2008
-L3S378 ATCGATCTGTGG GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 2 Yes 0 2_R_Palm_10_28_2008
-L3S294 CACGACAGGCTA GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 1 No 84 1_R_Palm_1_20_2009
-L4S63 CTCGTGGAGTAG GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 2 No 84 2_R_Palm_1_20_2009
-L3S313 AGTGTCACGGTG GTGCCAGCMGCCGCGGTAA right palm 2009 2 17 1 No 112 1_R_Palm_2_17_2009
-L3S341 CAAGTGAGAGAG GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 1 No 140 1_R_Palm_3_17_2009
-L4S112 GCGTTACACACA GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 2 No 140 2_R_Palm_3_17_2009
-L3S360 CATCGTATCAAC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 1 No 168 1_R_Palm_4_14_2009
-L4S137 GAACTGTATCTC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 2 No 168 2_R_Palm_4_14_2009
-L5S104 CAGTGTCAGGAC GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 1 Yes 0 1_Tong_10_28_2008
-L5S240 CTGGACTCATAG GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 2 Yes 0 2_Tong_10_28_2008
-L5S155 ATCTTAGACTGC GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 1 No 84 1_Tong_1_20_2009
-L6S20 GAGGCTCATCAT GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 2 No 84 2_Tong_1_20_2009
-L5S174 CAGACATTGCGT GTGCCAGCMGCCGCGGTAA tongue 2009 2 17 1 No 112 1_Tong_2_17_2009
-L5S203 CGATGCACCAGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 1 No 140 1_Tong_3_17_2009
-L6S68 GATACGTCCTGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 2 No 140 2_Tong_3_17_2009
-L5S222 CTAGAGACTCTT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 1 No 168 1_Tong_4_14_2009
-L6S93 GATTAGCACTCT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 2 No 168 2_Tong_4_14_2009
\ No newline at end of file

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/map.txt Sat Aug 05 07:33:48 2017 -0400

b'@@ -0,0 +1,1 @@\n+#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tDescription\rs1\tCTACCGATTGCG\tCCGGACTACHVGGGTWTCTAAT\ts1\rs2\tTCACCCAAGGTA\tCCGGACTACHVGGGTWTCTAAT\ts2\rs3\tAGCCAGTCATAC\tCCGGACTACHVGGGTWTCTAAT\ts3\rs4\tTAACGGCGCTCT\tCCGGACTACHVGGGTWTCTAAT\ts4\rs5\tGTTTGCTCGAGA\tCCGGACTACHVGGGTWTCTAAT\ts5\rs6\tCAAACGCACTAA\tCCGGACTACHVGGGTWTCTAAT\ts6\rs7\tGAACAAAGAGCG\tCCGGACTACHVGGGTWTCTAAT\ts7\rs8\tGCTAAGTGATGT\tCCGGACTACHVGGGTWTCTAAT\ts8\rs9\tAAGGGACAAGTG\tCCGGACTACHVGGGTWTCTAAT\ts9\rs10\tAGTGTCGATTCG\tCCGGACTACHVGGGTWTCTAAT\ts10\rs11\tCTATTAAGCGGC\tCCGGACTACHVGGGTWTCTAAT\ts11\rs12\tCCTACCATTGTT\tCCGGACTACHVGGGTWTCTAAT\ts12\rs13\tGAGTCCGTTGCT\tCCGGACTACHVGGGTWTCTAAT\ts13\rs14\tGATAACTGTACG\tCCGGACTACHVGGGTWTCTAAT\ts14\rs15\tTAAACCTGGACA\tCCGGACTACHVGGGTWTCTAAT\ts15\rs16\tCCGAATTGACAA\tCCGGACTACHVGGGTWTCTAAT\ts16\rs17\tCTGGCATCTAGC\tCCGGACTACHVGGGTWTCTAAT\ts17\rs18\tGGTGGTCGTTCT\tCCGGACTACHVGGGTWTCTAAT\ts18\rs19\tACTATGGGCTAA\tCCGGACTACHVGGGTWTCTAAT\ts19\rs20\tGCATTGAGTTCG\tCCGGACTACHVGGGTWTCTAAT\ts20\rs21\tGTTGCTGAGTCC\tCCGGACTACHVGGGTWTCTAAT\ts21\rs22\tCTATGGTGAACC\tCCGGACTACHVGGGTWTCTAAT\ts22\rs23\tGGACCAAGGGAT\tCCGGACTACHVGGGTWTCTAAT\ts23\rs24\tGTATTGGTCAGA\tCCGGACTACHVGGGTWTCTAAT\ts24\rs25\tAGAACCGTCATA\tCCGGACTACHVGGGTWTCTAAT\ts25\rs26\tAACTGGAACCCT\tCCGGACTACHVGGGTWTCTAAT\ts26\rs27\tATACTCGGCTGC\tCCGGACTACHVGGGTWTCTAAT\ts27\rs28\tACGCTTAACGAC\tCCGGACTACHVGGGTWTCTAAT\ts28\rs29\tAGCTTACCGACC\tCCGGACTACHVGGGTWTCTAAT\ts29\rs30\tAGGGCTATAGTT\tCCGGACTACHVGGGTWTCTAAT\ts30\rs31\tTGTCTCGCAAGC\tCCGGACTACHVGGGTWTCTAAT\ts31\rs32\tCAGCCGCATATC\tCCGGACTACHVGGGTWTCTAAT\ts32\rs33\tGATACGTTCGCA\tCCGGACTACHVGGGTWTCTAAT\ts33\rs34\tCCAAGATTCGCC\tCCGGACTACHVGGGTWTCTAAT\ts34\rs35\tGAGGCTGATTTA\tCCGGACTACHVGGGTWTCTAAT\ts35\rs36\tGAGTTAGCATCA\tCCGGACTACHVGGGTWTCTAAT\ts36\rs37\tTGTAGTATAGGC\tCCGGACTACHVGGGTWTCTAAT\ts37\rs38\tCTCACGCAATGC\tCCGGACTACHVGGGTWTCTAAT\ts38\rs39\tGTCCCGTGAAAT\tCCGGACTACHVGGGTWTCTAAT\ts39\rs40\tGGACAGTGTATT\tCCGGACTACHVGGGTWTCTAAT\ts40\rs41\tACACGACTATAG\tCCGGACTACHVGGGTWTCTAAT\ts41\rs42\tGTGTAGGTGCTT\tCCGGACTACHVGGGTWTCTAAT\ts42\rs43\tTGAACTAGCGTC\tCCGGACTACHVGGGTWTCTAAT\ts43\rs44\tTCCGAGTCACCA\tCCGGACTACHVGGGTWTCTAAT\ts44\rs45\tTCCTCTTTGGTC\tCCGGACTACHVGGGTWTCTAAT\ts45\rs46\tTCCACCCTCTAT\tCCGGACTACHVGGGTWTCTAAT\ts46\rs47\tTCGTGACGCTAA\tCCGGACTACHVGGGTWTCTAAT\ts47\rs48\tACGGCTAGTTCC\tCCGGACTACHVGGGTWTCTAAT\ts48\rs49\tGCACTGGCATAT\tCCGGACTACHVGGGTWTCTAAT\ts49\rs50\tGGCATTAGTTGA\tCCGGACTACHVGGGTWTCTAAT\ts50\rs51\tCGGTAGTTGATC\tCCGGACTACHVGGGTWTCTAAT\ts51\rs52\tTGAAAGCGGCGA\tCCGGACTACHVGGGTWTCTAAT\ts52\rs53\tGGTTACGGTTAC\tCCGGACTACHVGGGTWTCTAAT\ts53\rs54\tACATCAGGTCAC\tCCGGACTACHVGGGTWTCTAAT\ts54\rs55\tGTTGATACGATG\tCCGGACTACHVGGGTWTCTAAT\ts55\rs56\tCAGACACTTCCG\tCCGGACTACHVGGGTWTCTAAT\ts56\rs57\tTCACCATCCGAG\tCCGGACTACHVGGGTWTCTAAT\ts57\rs58\tACCCACCACTAG\tCCGGACTACHVGGGTWTCTAAT\ts58\rs59\tCAGAAGGTGTGG\tCCGGACTACHVGGGTWTCTAAT\ts59\rs60\tGAAGCTTGAATC\tCCGGACTACHVGGGTWTCTAAT\ts60\rs61\tACTAGGATCAGT\tCCGGACTACHVGGGTWTCTAAT\ts61\rs62\tGCTCCTTAGAAG\tCCGGACTACHVGGGTWTCTAAT\ts62\rs63\tTCCCATTCCCAT\tCCGGACTACHVGGGTWTCTAAT\ts63\rs64\tTGGCGTCATTCG\tCCGGACTACHVGGGTWTCTAAT\ts64\rs65\tAATCCTCGGAGT\tCCGGACTACHVGGGTWTCTAAT\ts65\rs66\tCTGGACGCATTA\tCCGGACTACHVGGGTWTCTAAT\ts66\rs67\tACCGATTAGGTA\tCCGGACTACHVGGGTWTCTAAT\ts67\rs68\tATGTGCTGCTCG\tCCGGACTACHVGGGTWTCTAAT\ts68\rs69\tTACGTACGAAAC\tCCGGACTACHVGGGTWTCTAAT\ts69\rs70\tATCACATTCTCC\tCCGGACTACHVGGGTWTCTAAT\ts70\rs71\tAGCCTGGTACCT\tCCGGACTACHVGGGTWTCTAAT\ts71\rs72\tGCTAAAGTCGTA\tCCGGACTACHVGGGTWTCTAAT\ts72\rs73\tTCTCAGCGCGTA\tCCGGACTACHVGGGTWTCTAAT\ts73\rs74\tGACCCTAGACCT\tCCGGACTACHVGGGTWTCTAAT\ts74\rs75\tTATTCAGCGGAC\tCCGGACTACHVGGGTWTCTAAT\ts75\rs76\tGTTCCGGATTAG\tCCGGACTACHVGGGTWTCTAAT\ts76\rs77\tGCGTGTAATTAG\tCCGGACTACHVGGGTWTCTAAT\ts77\rs78\tCTGTAGCTTGGC\tCCGGACTACHVGGGTWTCTAAT\ts78\rs79\tATGCCTCGTAAG\tCCGGACTACHVGGGTWTCTAAT\ts79\rs80\tACCTATGGTGAA\tCCGGACTACHVGGGTWTCTAAT\ts80\rs81\tCTGTTACAGCGA\tCCGGACTACHVGGGTWTCTAAT\ts81\rs82\tCAGTCAGGCCTT\tCCGGACTACHVGGGTWTCTAAT\ts82\rs83\tACTGAGCTGCAT\tCCGGACTACHVGGGTWTCTAAT\ts83\rs84\tACGAAGTCTACC\tCCGGACTACHVGGGTWTCTAAT\ts84\rs85\tACCGTCTTTCTC\tCCGGACTACHVGGGTWTCTAAT\ts85\rs86\tAGTCTGTCTGCG\tCCGGACTACHVGGGTWTCTAAT\ts86\rs87\tCCGCACTCAAGT\tCCGGACTACHVGGGTWTCTAAT\ts87\rs88\tTGTGGAAACTCC\tCCGGACTACHVGGGTWTCTAAT\ts88\rs89\tTTAGGCAGGTTC\tCCGGACTACHVGGGTWTCTAAT\ts89\rs90\tTAAGACTACTGG\tCCGGACTA'..b'GTWTCTAAT\ts106\rs107\tTGGAGAGGAGAT\tCCGGACTACHVGGGTWTCTAAT\ts107\rs108\tCGTATAAATGCG\tCCGGACTACHVGGGTWTCTAAT\ts108\rs109\tAATACAGACCTG\tCCGGACTACHVGGGTWTCTAAT\ts109\rs110\tGACTCAACCAGT\tCCGGACTACHVGGGTWTCTAAT\ts110\rs111\tGGAAGAAGTAGC\tCCGGACTACHVGGGTWTCTAAT\ts111\rs112\tATCGATCCACAG\tCCGGACTACHVGGGTWTCTAAT\ts112\rs113\tACACCGCACAAT\tCCGGACTACHVGGGTWTCTAAT\ts113\rs114\tGTCTCCTCCCTT\tCCGGACTACHVGGGTWTCTAAT\ts114\rs115\tGTAGCACTCATG\tCCGGACTACHVGGGTWTCTAAT\ts115\rs116\tCACCTGTAGTAG\tCCGGACTACHVGGGTWTCTAAT\ts116\rs117\tCACGAGCTACTC\tCCGGACTACHVGGGTWTCTAAT\ts117\rs118\tTCTCGATAAGCG\tCCGGACTACHVGGGTWTCTAAT\ts118\rs119\tTAGACACCGTGT\tCCGGACTACHVGGGTWTCTAAT\ts119\rs120\tAGACAAGCTTCC\tCCGGACTACHVGGGTWTCTAAT\ts120\rs121\tTCCGCAACCTGA\tCCGGACTACHVGGGTWTCTAAT\ts121\rs122\tTCACTTGGTGCG\tCCGGACTACHVGGGTWTCTAAT\ts122\rs123\tTTATGTACGGCG\tCCGGACTACHVGGGTWTCTAAT\ts123\rs124\tTTGGACGTCCAC\tCCGGACTACHVGGGTWTCTAAT\ts124\rs125\tTCCAGGGCTATA\tCCGGACTACHVGGGTWTCTAAT\ts125\rs126\tGCGTAGAGAGAC\tCCGGACTACHVGGGTWTCTAAT\ts126\rs127\tGAAACTCCTAGA\tCCGGACTACHVGGGTWTCTAAT\ts127\rs128\tATCGGGCTTAAC\tCCGGACTACHVGGGTWTCTAAT\ts128\rs129\tTACGCCCATCAG\tCCGGACTACHVGGGTWTCTAAT\ts129\rs130\tAAGATCGTACTG\tCCGGACTACHVGGGTWTCTAAT\ts130\rs131\tACTCATCTTCCA\tCCGGACTACHVGGGTWTCTAAT\ts131\rs132\tGAGATACAGTTC\tCCGGACTACHVGGGTWTCTAAT\ts132\rs133\tGCATGCATCCCA\tCCGGACTACHVGGGTWTCTAAT\ts133\rs134\tGATCTAATCGAG\tCCGGACTACHVGGGTWTCTAAT\ts134\rs135\tAATCTTGCGCCG\tCCGGACTACHVGGGTWTCTAAT\ts135\rs136\tGGAAATCCCATC\tCCGGACTACHVGGGTWTCTAAT\ts136\rs137\tGACCGTCAATAC\tCCGGACTACHVGGGTWTCTAAT\ts137\rs138\tTTGGAACGGCTT\tCCGGACTACHVGGGTWTCTAAT\ts138\rs139\tTCCTAGGTCCGA\tCCGGACTACHVGGGTWTCTAAT\ts139\rs140\tTCCTCACTATCA\tCCGGACTACHVGGGTWTCTAAT\ts140\rs141\tGCCTGCAGTACT\tCCGGACTACHVGGGTWTCTAAT\ts141\rs142\tGCCCAAGTTCAC\tCCGGACTACHVGGGTWTCTAAT\ts142\rs143\tATAAAGAGGAGG\tCCGGACTACHVGGGTWTCTAAT\ts143\rs144\tGCGCCGAATCTT\tCCGGACTACHVGGGTWTCTAAT\ts144\rs145\tATCCCAGCATGC\tCCGGACTACHVGGGTWTCTAAT\ts145\rs146\tGCTTCCAGACAA\tCCGGACTACHVGGGTWTCTAAT\ts146\rs147\tACACAGTCCTGA\tCCGGACTACHVGGGTWTCTAAT\ts147\rs148\tATTATACGGCGC\tCCGGACTACHVGGGTWTCTAAT\ts148\rs149\tATTCAGATGGCA\tCCGGACTACHVGGGTWTCTAAT\ts149\rs150\tTAAACGCGACTC\tCCGGACTACHVGGGTWTCTAAT\ts150\rs151\tCCTCGGGTACTA\tCCGGACTACHVGGGTWTCTAAT\ts151\rs152\tTTCACCTGTATC\tCCGGACTACHVGGGTWTCTAAT\ts152\rs153\tCTCCAGGTCATG\tCCGGACTACHVGGGTWTCTAAT\ts153\rs154\tCAGGATTCGTAC\tCCGGACTACHVGGGTWTCTAAT\ts154\rs155\tCGCATACGACCT\tCCGGACTACHVGGGTWTCTAAT\ts155\rs156\tGCCTCGTACTGA\tCCGGACTACHVGGGTWTCTAAT\ts156\rs157\tACCAACAGATTG\tCCGGACTACHVGGGTWTCTAAT\ts157\rs158\tGTGGCCTACTAC\tCCGGACTACHVGGGTWTCTAAT\ts158\rs159\tTTCCCTTCTCCG\tCCGGACTACHVGGGTWTCTAAT\ts159\rs160\tCATTTGACGACG\tCCGGACTACHVGGGTWTCTAAT\ts160\rs161\tAAGTGAAGCGAG\tCCGGACTACHVGGGTWTCTAAT\ts161\rs162\tTGCCGCCGTAAT\tCCGGACTACHVGGGTWTCTAAT\ts162\rs163\tAACCTCGGATAA\tCCGGACTACHVGGGTWTCTAAT\ts163\rs164\tGTGCTTGTGTAG\tCCGGACTACHVGGGTWTCTAAT\ts164\rs165\tCAACTAGACTCG\tCCGGACTACHVGGGTWTCTAAT\ts165\rs166\tAGTGCCCTTGGT\tCCGGACTACHVGGGTWTCTAAT\ts166\rs167\tGGAACGACGTGA\tCCGGACTACHVGGGTWTCTAAT\ts167\rs168\tTGTCAGCTGTCG\tCCGGACTACHVGGGTWTCTAAT\ts168\rs169\tCTGGTGCTGAAT\tCCGGACTACHVGGGTWTCTAAT\ts169\rs170\tGACAGAGGTGCA\tCCGGACTACHVGGGTWTCTAAT\ts170\rs171\tTCAGACCAACTG\tCCGGACTACHVGGGTWTCTAAT\ts171\rs172\tAGTGATGTGACT\tCCGGACTACHVGGGTWTCTAAT\ts172\rs173\tCTTAGCTACTCT\tCCGGACTACHVGGGTWTCTAAT\ts173\rs174\tTCGGTCCATAGC\tCCGGACTACHVGGGTWTCTAAT\ts174\rs175\tCACGTTTATTCC\tCCGGACTACHVGGGTWTCTAAT\ts175\rs176\tGAAACGGAAACG\tCCGGACTACHVGGGTWTCTAAT\ts176\rs177\tGGTCGTGTCTTG\tCCGGACTACHVGGGTWTCTAAT\ts177\rs178\tCGTCGTCTAAGA\tCCGGACTACHVGGGTWTCTAAT\ts178\rs179\tCAAGCGTTGTCC\tCCGGACTACHVGGGTWTCTAAT\ts179\rs180\tGACTTATGCCCG\tCCGGACTACHVGGGTWTCTAAT\ts180\rs181\tGTGACGTTAGTC\tCCGGACTACHVGGGTWTCTAAT\ts181\rs182\tGAGTCTTGGTAA\tCCGGACTACHVGGGTWTCTAAT\ts182\rs183\tTCGTCGCCAAAC\tCCGGACTACHVGGGTWTCTAAT\ts183\rs184\tAACATGCATGCC\tCCGGACTACHVGGGTWTCTAAT\ts184\rs185\tGTCTGTTGAGTG\tCCGGACTACHVGGGTWTCTAAT\ts185\rs186\tTGAGTTCGGTCC\tCCGGACTACHVGGGTWTCTAAT\ts186\rs187\tTTACGTGGCGAT\tCCGGACTACHVGGGTWTCTAAT\ts187\rs188\tCAATGCCTCACG\tCCGGACTACHVGGGTWTCTAAT\ts188\rs189\tTGTACGGATAAC\tCCGGACTACHVGGGTWTCTAAT\ts189\rs190\tAATCAACTAGGC\tCCGGACTACHVGGGTWTCTAAT\ts190\rs191\tGTGAGGGCAAGT\tCCGGACTACHVGGGTWTCTAAT\ts191\rs192\tCGTGGGCTCATT\tCCGGACTACHVGGGTWTCTAAT\ts192\n\\ No newline at end of file\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/seqs.fastq
--- a/test-data/split_libraries_fastq/seqs.fastq Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/seqs.fna
--- a/test-data/split_libraries_fastq/seqs.fna Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,172 +0,0 @@\n->L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGACATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATA\n->L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTG\n->L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTA\n->L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAG\n->L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTG\n->L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAG\n->L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGT\n->L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGG\n->L1S281_8 HWI-EAS440_0386:1:25:7669:2080#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCGACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAG\n->L1S140_9 HWI-EAS440_0386:1:25:3922:2110#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTT\n->L1S105_10 HWI-EAS440_0386:1:25:3806:2202#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAG\n->L1S76_11 HWI-EAS440_0386:1:25:6540:2228#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGAAGGCTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGGTCATCTA\n->L1S281_12 HWI-EAS440_0386:1:25:2668:2254#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTT\n->L1S76_13 HWI-EAS440_0386:1:25:5054:2329#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTG\n->L1S208_14 HWI-EAS440_0386:1:25:8482:2380#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAG\n->L1S208_15 HWI-EAS440_0386:1:25:8261:2388#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAG\n->L1S105_16 HWI-EAS440_0386:1:25:9735:2401#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAG\n->L1S8_17 HWI-EAS440_0386:1:25:8948:2437#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACG'..b'GATACTGGATATCTTGAGTGCAGTTGAGGCAGG\n->L1S140_69 HWI-EAS440_0386:1:25:4994:3354#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAG\n->L1S140_70 HWI-EAS440_0386:1:25:12091:3381#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGG\n->L1S105_71 HWI-EAS440_0386:1:25:8594:3395#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTT\n->L1S281_72 HWI-EAS440_0386:1:25:2052:3400#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTAGGAC\n->L1S76_73 HWI-EAS440_0386:1:25:11776:3405#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAG\n->L1S76_74 HWI-EAS440_0386:1:25:11052:3431#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGA\n->L1S105_75 HWI-EAS440_0386:1:25:9796:3444#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTGAGGCTAGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTG\n->L1S8_76 HWI-EAS440_0386:1:25:2235:3462#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAGTCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCA\n->L1S57_77 HWI-EAS440_0386:1:25:6708:3509#0/1 orig_bc=ACACACTATGGC new_bc=ACACACTATGGC bc_diffs=0\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAG\n->L1S281_78 HWI-EAS440_0386:1:25:13919:3507#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGG\n->L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n->L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTG\n->L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGG\n->L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAG\n->L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCG\n->L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAG\n->L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGG\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/seqs.qual
--- a/test-data/split_libraries_fastq/seqs.qual Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,584 +0,0 @@\n->L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n-[32 34 34 34 38 38 38 38 31 38 30 38 38 38 38 38 38 38 38 35 38 38 38 38 38\n- 38 38 38 38 38 38 38 38 38 38 38 35 38 38 33 38 38 38 33 38 38 38 38 38 38\n- 38 35 38 36 38 38 35 35 38 31 38 38 38 38 36 36 36 38 38 38 38 38 38 18 23\n- 23 38 35 29 35 35 38 38 36 36 31 35 35 35 35 33 29 37 35 38 35 29 31 12 25\n- 22 19 28 26 32 9 22 19 28 28 28 28 30 33 33 35 31]\n->L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n-[38 38 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39\n- 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 37\n- 39 33 39 39 36 34 34 39 33 35 39 37 36 39 32 36 31 31 33 35 33 28 33 31 31\n- 32 17 35 7 20 20 20 18 35 32 32 32 32 36 31 36 36 32 29 26 8 24 26 28 28\n- 32 29 22 33 31 28 31 22 23 26 25 23 17 30 34 27 29 27 24 30 27 29 29 29 24\n- 23 28 31]\n->L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n-[40 40 40 38 40 40 40 40 38 40 40 40 40 40 38 40 40 39 40 35 40 39 40 39 39\n- 37 31 40 40 37 40 40 40 40 40 38 40 40 40 39 40 39 38 39 33 40 40 40 38 39\n- 39 38 40 37 36 36 36 37 39 39 39 35 36 36 35 38 29 35 33 36 37 33 35 33 31\n- 33 33 28 36 36 33 33 33 36 38 36 35 35 33 32 29 35 31 31 31 31 33 34 33 33\n- 26 33 35 31 31 29 25 31 31 29 33 31 30 28 16 31 31 31 18 27 24 22 21 22 28\n- 21 29 26 26 30]\n->L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-[40 40 40 40 40 38 40 40 40 40 40 40 40 38 40 40 40 40 40 40 40 40 40 40 40\n- 37 40 40 38 36 38 38 35 40 40 40 40 40 37 37 39 40 40 38 35 38 36 38 35 29\n- 38 35 38 40 40 36 40 38 40 40 37 39 29 38 33 35 35 38 37 38 38 36 38 33 33\n- 17 35 33 35 35 38 33 35 36 33 36 33 33 23 30 27 33 29 33 29 32 31 35 28 18\n- 23 28 32 34 29 30 29 31 31 30 35 35 31 29 28 30 28 19 22 23 26 10 26 33 36\n- 23 29 33]\n->L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-[40 40 40 40 40 39 40 40 40 40 40 40 39 36 36 40 40 36 40 40 40 40 40 40 38\n- 38 39 40 39 36 40 40 39 35 37 34 40 38 39 39 39 34 36 35 33 40 36 40 36 36\n- 39 33 33 36 33 33 36 40 39 38 38 38 38 38 35 39 38 38 36 36 38 35 38 30 27\n- 17 32 20 35 33 33 33 33 36 33 36 33 33 33 31 33 36 35 36 33 33 33 36 26 31\n- 31 31 33 31 31 23 25 31 33 31 31 31 31 32 36 31 31 32 15 31 29 28 27 24 25\n- 26 24 28 22 29 25 26 28 28 27 30]\n->L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-[39 39 39 38 38 36 38 36 38 38 38 38 38 39 39 39 39 39 39 39 38 39 39 38 38\n- 34 38 38 39 37 39 39 39 39 39 39 39 39 36 35 33 38 38 39 37 39 39 39 39 37\n- 39 39 39 39 39 37 39 39 39 39 39 36 33 37 34 36 36 35 37 37 37 35 36 28 26\n- 31 34 28 34 34 34 32 32 33 33 35 31 31 25 28 26 30 28 33 33 31 29 35 33 35\n- 28 31 35 33 33 33 28 35 21 6 28 26 26 32 28 30 28 24 24 28 24 13 24 13 17\n- 11 14 17 28 28 28 22 24 31 31 21 31]\n->L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-[40 40 40 40 40 40 40 40 38 40 40 40 35 38 40 40 40 37 40 40 39 40 40 40 40\n- 40 40 40 40 40 40 40 40 40 40 36 40 37 38 37 38 38 38 39 40 40 38 40 40 40\n- 39 33 39 40 39 38 40 38 40 39 40 31 36 38 31 36 38 37 37 40 37 36 35 37 33\n- 34 27 37 36 34 31 33 10 31 33 33 33 33 23 17 28 28 30 33 33 31 27 33 33 31\n- 33 33 8 32 32 31 23 28 31 30 31 31 20 30 27 29 28 26 26 17 30 12 30 28 32\n- 30]\n->L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-[40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40\n- 33 40 40 40 38 40 40 40 40 40 40 40 40 40 40 37 40 40 40 40 40 40 40 40 40\n- 40 40 39 38 40 40 40 40 40 40 40 36 35 38 37 38 36 35 35 38 35 33 38 25 31\n- 31 36 34 38 36 37 36 33 39 33 39 37 39 33 33 31 31 38 38 33 33 33 35 33 36\n- 34 33 33 38 36 34 33 36 34 33 37 36 33 35 36 33 36 33 33 31 31 17 33 19 30\n- 27 28 30 26 32 30 3'..b' 40 40 40 40 39 40 40 37 40 40 40 38 38 39 40 40 39 40 35 40 39 40 40 38\n- 33 40 40 40 36 40 40 40 39 39 36 40 40 39 36 38 39 39 39 36 39 38 40 35 33\n- 36 38 33 40 37 36 37 37 36 36 39 36 33 39 36 37 34 39 38 38 39 36 39 36 31\n- 33 39 33 37 35 37 36 36 38 36 35 35 36 33 33 33 39 36 31 35 33 33 35 33 36\n- 33 33 36 35 36 36 35 33 36 29 32 36 34 35 34 35 33 31 33 33 31 25 34 31 33\n- 33 31 33 28 15 28 15 29 30 28 29 31]\n->L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-[40 40 40 40 40 40 40 39 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 40\n- 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 39 40 37 40 40 40 40 40 39 39\n- 40 37 40 40 40 39 38 39 39 40 39 40 40 40 39 39 40 40 37 37 40 34 40 33 23\n- 33 35 38 35 31 35 33 32 34 37 36 35 38 34 36 36 33 37 37 37 34 33 33 33 36\n- 33 36 33 32 32 26 23 30 29 30 32 32 32 33 33 34 34 31 33 33 29 29 34 31 35\n- 33 31 33 31 22 31 31 31 23 18 26 23 31 23 24 27 22 10 28 23 28 7 28 20 30\n- 24 30]\n->L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-[27 31 31 38 38 38 38 38 38 38 33 38 38 38 38 38 38 38 38 38 38 38 38 38 38\n- 38 38 38 38 38 38 35 36 38 38 38 38 38 38 38 38 38 38 38 33 38 38 38 38 38\n- 38 35 38 38 38 33 27 33 38 38 38 38 38 38 38 38 38 38 29 27 38 38 38 35 38\n- 35 38 38 38 36 38 35 38 38 38 38 38 36 38 37 36 27 35 38 35 35 35 35 38 38\n- 38 33 38 35 35 38 35 25 33 33 35 35 35 30 30 25 27 30 38 38 35 33 33 26 33]\n->L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-[40 40 40 38 40 40 40 40 38 39 40 40 38 38 40 40 40 40 40 39 40 40 40 40 39\n- 40 39 40 40 40 39 40 40 40 40 36 40 36 40 37 37 38 38 38 40 37 40 39 40 40\n- 39 37 40 39 40 39 35 37 40 40 40 38 36 39 36 39 39 40 39 40 38 38 37 36 38\n- 38 27 39 36 38 33 35 29 31 29 32 35 32 36 36 36 31 35 30 32 28 27 28 31 33\n- 31 31 31 33 31 33 29 33 33 33 33 34 32 31 31 8 29 31 27 19 29 16 29 31 31\n- 29 26 29 32 19 25 31 32]\n->L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n-[40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40\n- 35 40 40 40 40 40 40 40 40 40 39 40 40 39 40 40 40 40 40 39 40 40 40 39 35\n- 40 37 40 40 40 40 40 40 40 40 40 40 39 40 38 40 38 40 39 39 40 36 40 37 37\n- 36 40 36 40 39 40 37 40 38 38 39 38 39 35 39 39 39 38 39 38 33 27 36 36 35\n- 39 36 37 38 38 39 33 38 36 35 39 39 39 33 34 33 36 33 36 36 35 31 33 23 31\n- 31 31 32 31 33 31 31 31 23 30 18 30]\n->L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n-[40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 39\n- 38 40 40 40 39 40 40 40 40 40 40 40 40 40 39 39 40 40 40 40 40 38 37 40 40\n- 40 40 40 40 40 40 40 40 40 40 40 39 38 40 37 37 38 40 37 40 40 37 40 38 39\n- 33 40 39 38 40 39 40 38 39 38 38 36 35 35 33 35 33 37 35 29 33 31 31 33 33\n- 33 28 33 33 35 33 30 31 33 25 33 33 33 36 36 36 34 33 30 30 32 19 31 19 30\n- 28 28 30]\n->L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n-[28 33 31 38 35 38 38 38 36 38 36 38 38 38 38 38 38 38 38 36 38 38 38 38 38\n- 35 38 38 38 38 36 36 36 38 38 38 33 38 38 38 38 38 38 38 35 38 38 38 38 38\n- 38 38 31 36 36 33 33 36 30 30 30 35 33 38 38 38 36 38 33 38 38 35 38 38 38\n- 38 33 34 30 15 30 27 33 37 38 37 29 33 35 38 35 35 38 34 33 35 35 35 35 35\n- 35 35 35 36 38 38 37 35 35 35 32 38 10 7 17 25 18 24 35 33 32 32 32]\n->L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n-[40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 37\n- 37 40 40 40 37 40 40 40 40 40 39 40 40 40 39 36 40 40 40 39 40 40 40 39 39\n- 40 37 40 40 40 40 39 40 40 40 39 39 39 40 38 39 39 37 39 40 39 36 40 35 33\n- 33 37 38 39 37 39 37 36 39 36 40 40 36 33 35 33 36 36 35 34 35 36 37 28 35\n- 33 35 35 34 33 35 28 35 31 33 35 36 33 35 37 34 34 29 33 31 33 19 33 28 31\n- 28 29 31 28 33 33 29 23 30]\n'

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/sequence_qualities.qual
--- a/test-data/split_libraries_fastq/sequence_qualities.qual Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r d44bd2602944 -r 4e9b6a0fcb78 test-data/split_libraries_fastq/sequences.fasta
--- a/test-data/split_libraries_fastq/sequences.fasta Mon Jul 10 16:44:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r d44bd2602944 -r 4e9b6a0fcb78 upgma_cluster.xml
--- a/upgma_cluster.xml Mon Jul 10 16:44:06 2017 -0400
+++ b/upgma_cluster.xml Sat Aug 05 07:33:48 2017 -0400

[

@@ -1,22 +1,22 @@
-<tool id="qiime_upgma_cluster" name="Build UPGMA tree" version="@WRAPPER_VERSION@.0">
-    <description>comparing samples</description>
+<tool id="qiime_upgma_cluster" name="Build a UPGMA tree" version="@WRAPPER_VERSION@.0">
+    <description> comparing samples (upgma_cluster)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>upgma_cluster.py -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        mkdir input
-        &&
-        #for $i, $matrix in enumerate($input_path)
-            cp '$matrix' 'input/dataset_$i' &&
-        #end for
-        upgma_cluster.py
-            --input_path input
-            --output_path output
+mkdir input
+&&
+#for $i, $matrix in enumerate($input_path)
+    cp '$matrix' 'input/dataset_$i' &&
+#end for
+upgma_cluster.py
+    --input_path input
+    --output_path output
     ]]></command>
     <inputs>
-        <param argument="--input_path" type="data" format="txt" label="Distance matrix" multiple="true"/>
+        <param argument="--input_path" type="data" format="txt" multiple="true" label="Distance matrix"/>
     </inputs>
     <outputs>
         <collection type="list" name="output_trees" label="${tool.name} on ${on_string}: UPGMA trees">