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Changeset 5:6b784a33f3b3 (2017-08-05)

Previous changeset 4:beee65df4180 (2017-07-10) Next changeset 6:1fe225d38243 (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
validate_mapping_file.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 beee65df4180 -r 6b784a33f3b3 generate_test_data.sh
--- a/generate_test_data.sh Mon Jul 10 16:40:50 2017 -0400
+++ b/generate_test_data.sh Sat Aug 05 07:27:55 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 beee65df4180 -r 6b784a33f3b3 macros.xml
--- a/macros.xml Mon Jul 10 16:40:50 2017 -0400
+++ b/macros.xml Sat Aug 05 07:27:55 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 beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/barcodes.fastq
--- a/test-data/split_libraries_fastq/barcodes.fastq Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/demultiplexed_sequences.fastq
--- a/test-data/split_libraries_fastq/demultiplexed_sequences.fastq Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/forward_reads.fastq
--- a/test-data/split_libraries_fastq/forward_reads.fastq Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/histograms.tabular
--- a/test-data/split_libraries_fastq/histograms.tabular Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/histograms.txt
--- a/test-data/split_libraries_fastq/histograms.txt Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/lane1_barcode.fastq.gz

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

diff -r beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/lane1_read1.fastq.gz

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

diff -r beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/lane2_barcode.fastq.gz

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

diff -r beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/lane2_read1.fastq.gz

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

diff -r beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/map.tsv
--- a/test-data/split_libraries_fastq/map.tsv Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 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 07:27:55 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/seqs.fastq
--- a/test-data/split_libraries_fastq/seqs.fastq Mon Jul 10 16:40:50 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/seqs.fna
--- a/test-data/split_libraries_fastq/seqs.fna Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/seqs.qual
--- a/test-data/split_libraries_fastq/seqs.qual Mon Jul 10 16:40:50 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 beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/sequence_qualities.qual
--- a/test-data/split_libraries_fastq/sequence_qualities.qual Mon Jul 10 16:40:50 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r beee65df4180 -r 6b784a33f3b3 test-data/split_libraries_fastq/sequences.fasta
--- a/test-data/split_libraries_fastq/sequences.fasta Mon Jul 10 16:40:50 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r beee65df4180 -r 6b784a33f3b3 validate_mapping_file.xml
--- a/validate_mapping_file.xml Mon Jul 10 16:40:50 2017 -0400
+++ b/validate_mapping_file.xml Sat Aug 05 07:27:55 2017 -0400

[

@@ -1,39 +1,39 @@
-<tool id="qiime_validate_mapping_file" name="Validate mapping file" version="@WRAPPER_VERSION@.0">
-    <description>to check for required data and format</description>
+<tool id="qiime_validate_mapping_file" name="Check user's metadata mapping file" version="@WRAPPER_VERSION@.0">
+    <description> for required data, valid format (validate_mapping_file)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>validate_mapping_file.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        validate_mapping_file.py
-            --mapping_fp '$mapping_fp'
-            -o validate_mapping_file_output
-            $verbose
-            --char_replace '$char_replace'
-            $not_barcoded
-            $variable_len_barcodes
-            $disable_primer_check
-            #if str($added_demultiplex_field):
-                --added_demultiplex_field '$added_demultiplex_field'
-            #end if
-            $suppress_html
+validate_mapping_file.py
+    --mapping_fp '$mapping_fp'
+    -o validate_mapping_file_output
+    $verbose
+    --char_replace '$char_replace'
+    $not_barcoded
+    $variable_len_barcodes
+    $disable_primer_check
+    #if str($added_demultiplex_field):
+        --added_demultiplex_field '$added_demultiplex_field'
+    #end if
+    $suppress_html

-            #if not $suppress_html:
-                && mkdir -p '$html_report.files_path'
-                && mv validate_mapping_file_output/*.html '$html_report'
-                && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
-            #end if
+    #if not $suppress_html:
+        && mkdir -p '$html_report.files_path'
+        && mv validate_mapping_file_output/*.html '$html_report'
+        && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
+    #end if
     ]]></command>
     <inputs>
-       <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt" help=""/>
-        <param argument="--verbose" type="boolean" label="Enable printing information to standard out?" truevalue="-v" falsevalue="" checked="False"/>
+       <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt"/>
+        <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Enable printing information to standard out?"/>
         <param argument="--char_replace" type="text" value="_" label="Default character used to replace invalid characters found in the mapping file" help="Must be a valid character (alphanumeric, period, or underscore)"/>
-        <param argument="--not_barcoded" type="boolean" label="Are barcodes present?" truevalue="" falsevalue="--not_barcoded" checked="True" help="BarcodeSequence header is still required in mapping file"/>
-        <param argument="--variable_len_barcodes" type="boolean" label="Are barcodes with variable length?" truevalue="" falsevalue="--variable_len_barcodes" checked="True" help=""/>
-        <param argument="--disable_primer_check" type="boolean" label="Disable checks for primers?" truevalue="-disable_primer_check" falsevalue="" checked="False" help="LinkerPrimerSequence header is still required in mapping file"/>
-        <param argument="--added_demultiplex_field" type="text" label="Field to use in the mapping file as additional demultiplexing (optional)" help="It can be used with or without barcodes.  All combinations of barcodes/primers and these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'" optional="True"/>
-        <param argument="--suppress_html" type="boolean" label="Disable html file generation?" truevalue="-s" falsevalue="" checked="False" help="It can be useful for extremely large mapping files"/>
+        <param argument="--not_barcoded" type="boolean" truevalue="" falsevalue="--not_barcoded" checked="true" label="Are barcodes present?" help="BarcodeSequence header is still required in mapping file"/>
+        <param argument="--variable_len_barcodes" type="boolean" truevalue="" falsevalue="--variable_len_barcodes" checked="true" label="Are barcodes with variable length?"/>
+        <param argument="--disable_primer_check" type="boolean" truevalue="-disable_primer_check" falsevalue="" checked="false" label="Disable checks for primers?" help="LinkerPrimerSequence header is still required in mapping file"/>
+        <param argument="--added_demultiplex_field" type="text" optional="true" label="Field to use in the mapping file as additional demultiplexing (optional)" help="It can be used with or without barcodes. All combinations of barcodes/primers and these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'"/>
+        <param argument="--suppress_html" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Disable html file generation?" help="It can be useful for extremely large mapping files"/>
     </inputs>
     <outputs>
         <data name="html_report" format="html" label="${tool.name} on ${on_string}: html report">