# HG changeset patch
# User pjbriggs
# Date 1538724628 14400
# Node ID 361f703e409450e9f57417ed8f845623708acfb0
# Parent  86bedbd3c5c28594b9d496a3103d266ce249b67f
Version 0.36.6

diff -r 86bedbd3c5c2 -r 361f703e4094 README.rst
--- a/README.rst	Mon Mar 05 05:33:13 2018 -0500
+++ b/README.rst	Fri Oct 05 03:30:28 2018 -0400
@@ -71,6 +71,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+0.36.6     - Added trimlog and log outputs; add support for ``fastqillumina``
+             and ``fastqsolexa`` input types
 0.36.5     - Remove tool_dependencies.xml and always use conda to resolve tool
              dependencies
 0.36.4     - Add option to provide custom adapter sequences for ILLUMINACLIP
@@ -110,10 +112,10 @@
 =======
 
 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs).
-Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed
+Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 
 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP.
-
+Matthias Bernt (@bernt-matthias) added log and trimlog output.
 
 Developers
 ==========
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/Illumina_SG_R1.fastqillumina
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R1.fastqillumina	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC
++
+^^^^^aaa_aaaa^aaeeeeBUUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbI^^b``ddbdY^db`Y^`I^dddd^dddd^O``bN^WHOOIIOYWFWZSWI^WNW^`ddddWY`IWIOYIIOIIY^b^SWO^dd^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG
++
+^^^^^aaacccc`cccd_eeBUUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeIY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dIWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbIY^IYW^dc[]WMHW^[
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA
++
+^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZH^``bbddd^``^Y^dWW`ddYbd^``ddddY^IIIOYI^^``dddddd`^MWZdBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA
++
+T\\\\]N[______]_bbbdBUU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddHWRbc\\_JS_cddI[cP[HP_ZWWWIXOZIPXWW_HQHFSZ\ddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG
++
+^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HWHY`W^db^WIIIOIOOYW^IHOIPY^b`bbY``^ZH^dde`ddbdWWIHP`IPOIPYIP^Y`bYY`HIYYIW`bddd^BBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA
++
+^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^bIPIIOPOYI^dWQFQ[fbdBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC
+GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA
++
+TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdIO^IIINYYY^YIN^Y`YYIINYIY`bd^OYYY`YYIIIOOYYIN^bWWW^^dddBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT
++
+^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IWHS`^`BBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG
++
+\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedII]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cIXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddFSSX^[[dZ\d[[ZWGUZ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
++
+\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/Illumina_SG_R1.fastqsolexa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R1.fastqsolexa	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC
++
+^^^^^aaa_aaaa^aaeeee>UUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbH^^b``ddbdY^db`Y^`H^dddd^dddd^O``bN^WGOOHHOYWEWZSWH^WNW^`ddddWY`HWHOYHHOHHY^b^SWO^dd^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG
++
+^^^^^aaacccc`cccd_ee>UUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeHY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dHWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbHY^HYW^dc[]WMGW^[
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA
++
+^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZG^``bbddd^``^Y^dWW`ddYbd^``ddddY^HHHOYH^^``dddddd`^MWZd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA
++
+T\\\\]N[______]_bbbd>UU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddGWRbc\\_JS_cddH[cP[GP_ZWWWHXOZHPXWW_GQGESZ\dd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG
++
+^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^H``dee^^]c^GWGY`W^db^WHHHOHOOYW^HGOHPY^b`bbY``^ZG^dde`ddbdWWHGP`HPOHPYHP^Y`bYY`GHYYHW`bddd^>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA
++
+^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^bHPHHOPOYH^dWQEQ[fbd>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC
+GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA
++
+TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdHO^HHHNYYY^YHN^Y`YYHHNYHY`bd^OYYY`YYHHHOOYYHN^bWWW^^ddd>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT
++
+^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HWGS`^`>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG
++
+\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedHH]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cHXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddESSX^[[dZ\d[[ZWFUZ^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
++
+\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/Illumina_SG_R2.fastqillumina
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R2.fastqillumina	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC
+GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT
++
+^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`IMSWMFOIPYY`^b``^bbYYSFFSFOOFWY^`W^dBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC
+GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC
++
+^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC
+GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA
++
+^^```aaacccccdccffbeffggheegggBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBUU^\BBSUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``FQQQW]IOIPbY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC
+GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA
++
+^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaaHHMHMY```dd^`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC
+TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG
++
+`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbFFWYbY^bbdI^HObbOYI^YbY^bbbW^bbdbXIYYbbbb^bIYYMbdffdbXXbSFHHMOOIYbY^IPOYbbBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC
+GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG
++
+^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZIYaZPZFFOYYOIPY`IYZ]ccFSFWMYY``]cQQ]c`]FFOMMOW^IY`IP^YIO^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC
+GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG
++
+^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^bPIOIPPMWbHQ^FSW]fBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC
+GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT
++
+^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc`FSQWbdY^XbbSWQW]FS[HOY]FOSHP^dIWYPbb^^HYbbddbbIIWHOTSW^bIY^YIOPOIYbbBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC
+GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT
++
+TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC
+GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC
++
+^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddIZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWHWY`bddd^dHSZ^Z^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/Illumina_SG_R2.fastqsolexa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R2.fastqsolexa	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC
+GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT
++
+^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`HMSWMEOHPYY`^b``^bbYYSEESEOOEWY^`W^d>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC
+GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC
++
+^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC
+GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA
++
+^^```aaacccccdccffbeffggheeggg>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>UU^\>>SUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``EQQQW]HOHPbY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC
+GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA
++
+^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaaGGMGMY```dd^`^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC
+TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG
++
+`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbEEWYbY^bbdH^GObbOYH^YbY^bbbW^bbdbXHYYbbbb^bHYYMbdffdbXXbSEGGMOOHYbY^HPOYbb>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC
+GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG
++
+^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZHYaZPZEEOYYOHPY`HYZ]ccESEWMYY``]cQQ]c`]EEOMMOW^HY`HP^YHO^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC
+GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG
++
+^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^bPHOHPPMWbGQ^ESW]f>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC
+GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT
++
+^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc`ESQWbdY^XbbSWQW]ES[GOY]EOSGP^dHWYPbb^^GYbbddbbHHWGOTSW^bHY^YHOPOHYbb>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC
+GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT
++
+TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC
+GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC
++
+^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddHZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWGWY`bddd^dGSZ^Z^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r1_paired_out1.fastqillumina
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,32 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNT
++
+^^^^^aaa_aaaa^aaeeeeBU
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNA
++
+^^^^^aaacccc`cccd_eeBU
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG
++
+^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNT
++
+T\\\\]N[______]_bbbdBU
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG
++
+^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HW
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA
++
+^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^b
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG
++
+^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IW
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGG
++
+\T\\\[]JT[
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,32 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNT
++
+^^^^^aaa_aaaa^aaeeee>U
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNA
++
+^^^^^aaacccc`cccd_ee>U
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG
++
+^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNT
++
+T\\\\]N[______]_bbbd>U
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTC
++
+^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA
++
+^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^b
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG
++
+^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HW
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGG
++
+\T\\\[]JT[
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r1_unpaired_out1.fastqillumina
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r1_unpaired_out1.fastqsolexa
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r2_paired_out1.fastqillumina
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,32 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC
+GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG
++
+^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC
+GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG
++
+^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC
+GAATATAGAAACGGGAGTATAGTGGTAACC
++
+^^```aaacccccdccffbeffggheeggg
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC
+GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC
++
+^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaa
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC
+TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA
++
+`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC
+GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT
++
+^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC
+GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG
++
+^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc`
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC
+GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG
++
+TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,32 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC
+GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG
++
+^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC
+GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG
++
+^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC
+GAATATAGAAACGGGAGTATAGTGGTAACC
++
+^^```aaacccccdccffbeffggheeggg
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC
+GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC
++
+^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaa
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC
+TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA
++
+`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC
+GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT
++
+^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC
+GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG
++
+^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc`
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC
+GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG
++
+TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,8 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC
+GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA
++
+^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^b
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC
+GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG
++
+^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,8 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC
+GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA
++
+^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^b
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC
+GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG
++
+^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_se_out1.err
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_se_out1.err	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,5 @@
+TrimmomaticSE: Started with arguments:
+ -threads 1 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog
+Quality encoding detected as phred33
+Input Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%)
+TrimmomaticSE: Completed successfully
diff -r 86bedbd3c5c2 -r 361f703e4094 test-data/trimmomatic_se_out1.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_se_out1.log	Fri Oct 05 03:30:28 2018 -0400
@@ -0,0 +1,10 @@
+MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC 22 0 22 228
+MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC 22 0 22 228
+MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC 113 0 113 137
+MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC 22 0 22 228
+MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC 161 0 161 89
+MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC 223 0 223 27
+MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC 0 0 0 0
+MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC 236 0 236 14
+MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC 10 0 10 240
+MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC 0 0 0 0
diff -r 86bedbd3c5c2 -r 361f703e4094 trimmomatic.xml
--- a/trimmomatic.xml	Mon Mar 05 05:33:13 2018 -0500
+++ b/trimmomatic.xml	Fri Oct 05 03:30:28 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.36.5">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.6">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>
@@ -24,12 +24,12 @@
   #end if
   java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
   #if $readtype.single_or_paired in ["pair_of_files","collection"]
-    PE -threads \${GALAXY_SLOTS:-6} -phred33
+    PE -threads \${GALAXY_SLOTS:-6}
       fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
       fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
       fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
   #else
-    SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
+    SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
   #end if
   ## ILLUMINACLIP option
   #if $illuminaclip.do_illuminaclip
@@ -76,6 +76,9 @@
       MAXINFO:$op.operation.target_length:$op.operation.strictness
     #end if
   #end for
+  #if $output_logs:
+    -trimlog trimlog
+  #end if
   2>&1 | tee trimmomatic.log &&
   if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
   &&
@@ -109,16 +112,16 @@
          <option value="collection">Paired-end (as collection)</option>
       </param>
     <when value="se">
-      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
+      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
     </when>
     <when value="pair_of_files">
-      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
+      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R1/first of pair)" />
-      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz"
+      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R2/second of pair)" />
     </when>
       <when value="collection">
-        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
+        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
       </when>
     </conditional>
     <conditional name="illuminaclip">
@@ -198,6 +201,8 @@
         </when>
       </conditional>
     </repeat>
+    <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
+    <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
   </inputs>
   <outputs>
     <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
@@ -225,15 +230,26 @@
         <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
         <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
     </collection>
-
+    <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
+      <filter>output_logs</filter>
+    </data>
+    <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">
+      <filter>output_err</filter>
+    </data>
   </outputs>
   <tests>
     <test>
       <!-- Single-end example -->
-      <param name="single_or_paired" value="se" />
-      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      <conditional name="readtype">
+        <param name="single_or_paired" value="se" />
+        <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      </conditional>
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <param name="output_logs" value="yes" />
+      <param name="output_err" value="yes" />
       <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
+      <output name="log_file" file="trimmomatic_se_out1.log" />
+      <output name="err_file" file="trimmomatic_se_out1.err" />
     </test>
     <test>
       <!-- Single-end example - gzipped -->
@@ -265,6 +281,28 @@
       <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
     </test>
     <test>
+      <!-- Paired-end Illumina 1.3-1.7 quality encoding -->
+      <param name="single_or_paired" value="pair_of_files" />
+      <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" />
+      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" />
+      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" />
+    </test>
+    <test>
+      <!-- Paired-end Solexa quality encoding -->
+      <param name="single_or_paired" value="pair_of_files" />
+      <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" />
+      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" />
+      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" />
+    </test>
+    <test>
       <!-- Single-end example (cropping) -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -435,7 +473,7 @@
 
 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
 University of Manchester, with contributions from Peter van Heusden, Marius
-van den Beek, Jelle Scholtalbers and Charles Girardot.
+van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt.
 
 It runs the Trimmomatic program which has been developed
 within Bjorn Usadel's group at RWTH Aachen university.