--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq	Mon Jan 13 14:57:53 2014 -0500
@@ -0,0 +1,200 @@
+@SOLEXA2_0414:3:1:11146:1065#0/1
+NTGCGATCAAGGGATAAGGGTGGGACACTGCGGGAGATTCAGAGTAACAGTTNTAAGGTCTGGTTTGTCCGGACACTGCGGNAGA
++SOLEXA2_0414:3:1:11146:1065#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:12658:1069#0/1
+NCTACATACAGTTGTAAGGTCTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTATGTAGCAGATCGGAAGAGNGGT
++SOLEXA2_0414:3:1:12658:1069#0/1
+BOIOKPTTTT_________________________________________________TYYYYY___________Q__BBBBBB
+@SOLEXA2_0414:3:1:17191:1069#0/1
+NAGCAATCTATAGTTTGTGTATTGCCAAGTCTGTTGTGAGCCCTTCCACAAGTTTTGTTTAGAGGAGAACGAGCGCCCTCTNGAT
++SOLEXA2_0414:3:1:17191:1069#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:6993:1073#0/1
+NTGGATCTCCCGCAGTGTCCTAAATGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGAC
++SOLEXA2_0414:3:1:6993:1073#0/1
+BJJJJVVVWVb__bb______bb________________b__________Y[[[[b__b__bb__YYYYY_______________
+@SOLEXA2_0414:3:1:10702:1075#0/1
+NCTACATTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACGACTGTTACTCTGAATCTCCCGCAGTGTCCTCTGC
++SOLEXA2_0414:3:1:10702:1075#0/1
+BIHKIQTQTQ[[[YPVTVVVWWWWVRRPRTVPTTTVVVTTVTVTVVVVVTTVVVVRRPLRTQTJQ_____YYVYYVVTNVXWWVW
+@SOLEXA2_0414:3:1:12096:1078#0/1
+NTGCGATTACTCTGAATCTCCCGCAGTGTCCAATACTGTACTTTTTTACATAGTCATTGCTTAATGAATATGTATTGAATTAAAT
++SOLEXA2_0414:3:1:12096:1078#0/1
+BEKEEJOHHHTTVVV_____[[Y[[WWVXXXVXXWRRPTTWXXXWWQQWXWWWTWKKLLLLLLHRVTVVNTTVVT_____YWYYY
+@SOLEXA2_0414:3:1:12624:1071#0/1
+NTGCGATAGTGTCCTGTGTGCCCCTGCACATGCCTGTGGCTTCCCGGGCTTCTGACCACATCCCCACCATCTTTGTGCCTCCGGA
++SOLEXA2_0414:3:1:12624:1071#0/1
+BQLLMTTTTT__________YYYYY________b___________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:13769:1080#0/1
+NAGCAATCTAAAACCCAAAGTATATAAGAAGGGTATGGTTGATTATGTTTTTCTACATATTATTTGACATACTTCTATCTTCCCA
++SOLEXA2_0414:3:1:13769:1080#0/1
+BPPPPXXXXX_b_b_b_bbb_b___YYYYYWXXXXWWWWW_b__b_____QQQQQb_b_b_b_bQQZ___b_b____________
+@SOLEXA2_0414:3:1:13956:1081#0/1
+NTGCGATCTCAGTCTCCTGAGTAGCTGGGATCTAGCACTCAGAAATGAGAGATGAAAAGGCTAATTCACAAAGTAGCCAAAAATA
++SOLEXA2_0414:3:1:13956:1081#0/1
+BPPPNWWWWW__b__b_bb_____b_b__b__b_bb_bbb______________bb_____b__bbb__bYYYWY________YO
+@SOLEXA2_0414:3:1:14801:1076#0/1
+NTGCGATGGACCAGCTGGAAAATTGGTGTTGTCGTCGGTGCAAATTCTGTCACGTTTGTGGAAGGCGACATCAGGCTACAAGGGG
++SOLEXA2_0414:3:1:14801:1076#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:16010:1079#0/1
+NAGCAATTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGT
++SOLEXA2_0414:3:1:16010:1079#0/1
+BKJQQVWVVV_______________WYYYY_______________V____Y[[[[_________________________BBBBB
+@SOLEXA2_0414:3:1:17165:1075#0/1
+NTGCGATCTAGGACACTGCGGGAGATTCAGAGTACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCAGAGTAACA
++SOLEXA2_0414:3:1:17165:1075#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:19504:1081#0/1
+NAGCAATACTTCTATCTTCCCATGTTCTTACTATAGTTTGTGTATTGCCAAGTCTGTTGTGAGCCACATAATAAGGTGTCAAAAT
++SOLEXA2_0414:3:1:19504:1081#0/1
+BJJOJRRQQRYYYYY__b_______[[[[PWWTWWYYYYY[Y[[[YYYYUTTWVVY[YY[_______________VTTTVTVVTV
+@SOLEXA2_0414:3:1:19703:1080#0/1
+NAGCAATATTGAATTAAATATATGCCAGTGGACTACTAAAACCCAAAGTATATAAGAAGGGTATGGTTGATTATGTTTTTCTACA
++SOLEXA2_0414:3:1:19703:1080#0/1
+BIKOIVWVVVY[Y[YVVTVTYYYYY_W___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:6962:1084#0/1
+NTGCGATCTGAATCTCCCGCAGTGTCCGGGTGGGGTCAGAAAAATGGGCAGCTCAACTGCAGGTACACGTAGTGCGACCAGTGCC
++SOLEXA2_0414:3:1:6962:1084#0/1
+BEMEEKLQJJ__________Y[[[[XXXXXXWQQQQYYYY__QQQ___PWWWXWV_____BBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:8715:1091#0/1
+NTGCGATCAACCATTCAGACACCAGCAGAAGTGTTCTGGAATCCTATGTGAGGGACATACATTCAGACCACGGCAGAAGTGTTCT
++SOLEXA2_0414:3:1:8715:1091#0/1
+BGKEEHMKHL[[[[[_____Y[[[[_______________W_________YYYYY_______________[[Y[Y[[[Y[[[[[[
+@SOLEXA2_0414:3:1:12077:1083#0/1
+NAGCAATATGCTTTGGCCACAAAATAAGTGCACTGTGCAATATCAAGTGTTTCAGCAAGTTTTTGGAATCTCAAGCACATTTTGA
++SOLEXA2_0414:3:1:12077:1083#0/1
+BJJJJQRPPObbb____b__b__QQQQQ_________b_____b_[[[[[______V_____________b____YY[[[b___O
+@SOLEXA2_0414:3:1:13392:1083#0/1
+NTGCGATCCGGACACTGCGGGAGATTCAGAGTAACAGTTGTAAGGTCTGGTTTGTCCTATTTGTGTTTGAATTTGGCTCTACGTG
++SOLEXA2_0414:3:1:13392:1083#0/1
+BKJQJORQPP_______________TWTWTWWWTTYYYYY_____YYYYWYYYYYYYYYYWWWWWVVTTV______Y_______B
+@SOLEXA2_0414:3:1:14856:1092#0/1
+NTGCGATGTGTCCTTAGGACAAACCAGACCTTACAACTGTAAGCCTGGCTTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGA
++SOLEXA2_0414:3:1:14856:1092#0/1
+BIIOHTTSTT_____[[[[YYYYYYVYYYY______________W[[[YY__________V[[[[____WXVVXX___W_XXWXV
+@SOLEXA2_0414:3:1:17070:1089#0/1
+NTGCGATCTGAATCTCCCGCAGTGTCCCACTCTTAGGTCACTTAGCATGTTCATTAGAGTACTCTGAATCTCCCGCAGTGTCCTC
++SOLEXA2_0414:3:1:17070:1089#0/1
+BHMOGRTTTTY[[[Y__________TVVVTYVYYY____WYYYYRPRWRR[[Y[[_____WWWTWWTWWWYYYYY[R[[YYYYYY
+@SOLEXA2_0414:3:1:18860:1082#0/1
+NAGCAATACAGTTGTAAGGTCTGGTTTGTCCTCACTCAAATGTCATCTCGAATTGTAGTTCTCATAATGGCCGCATGTTGTGGGA
++SOLEXA2_0414:3:1:18860:1082#0/1
+BHOKHSWTTT____________________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:18912:1089#0/1
+NTGCGATCATCTGAGGAGGACACTGCGGGAGATTCAGAGTAACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCA
++SOLEXA2_0414:3:1:18912:1089#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:3923:1105#0/1
+NAGCAATAGTCCAGGGATACAGAACCCACTGATACAGAGGCCCAGCTGTAGTTCTATTATTGCTCAGATCGGAAGAGCGGTTCAG
++SOLEXA2_0414:3:1:3923:1105#0/1
+BNNNQVWVVV__bbb__b_bb____b________b__Z_______[[[[YYYYYY_____b___bb____YWWYYVVTVVYYYYY
+@SOLEXA2_0414:3:1:6494:1099#0/1
+NTGCGATTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTACAGTTGTAAGGTCTGGTTTGTCCTAGGCAGAATCGC
++SOLEXA2_0414:3:1:6494:1099#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:8413:1097#0/1
+NTGCGATCCATACCCTTCTTATATACTTTGGGTTTTAGTAGTCCACTGGCATATATTTAATTCAATACATACTCATTAAGCAATG
++SOLEXA2_0414:3:1:8413:1097#0/1
+BGIGEMQLNQ_______________VXXXX_____WWXXX[YY[[_____WYRYY___________V___YLYYYYYYPY_____
+@SOLEXA2_0414:3:1:9865:1095#0/1
+NCTACATTAATTGTTTTAATTTTTATTTATTTATTTTTTTGAGACGGAGTCTCGCTGATGTAGCAGATCGGAAGAGCGGTTCAGC
++SOLEXA2_0414:3:1:9865:1095#0/1
+BKKJKRTTST_____QQQ_b[[[[[QQQQ_QQQbQQQQQQQ_________bb__________________[[[[Y__________
+@SOLEXA2_0414:3:1:10606:1102#0/1
+NTGCGATATTTGGAACTTCATGTGTCTTTTGTATTGCTTGATAGCAGCATAGAATATGTGAGGTATTTTTGGCTACTTTGTGAAT
++SOLEXA2_0414:3:1:10606:1102#0/1
+BMMMMTUTTRTTVWV_____b___b__b_QQQQ__[Y[[YYYYYY_______________[[[[[YYYQQQ____BBBBBBBBBB
+@SOLEXA2_0414:3:1:11267:1102#0/1
+NCTACATTACTCTGAATCTCCCGCAGTGTCCGAGATCGCACCACTGCACCCCAGCCTGGGCGACATGTAGCAGATCGGAAGAGCG
++SOLEXA2_0414:3:1:11267:1102#0/1
+BEGGEJLHIK______________RTWWWWY[Y[[________________QM__YYYYYXWJVX_____BBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:13556:1104#0/1
+NTGCGATTTACAACCGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTATCGCAAAGATCGGAAGAG
++SOLEXA2_0414:3:1:13556:1104#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:13625:1097#0/1
+NTGCGATCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTATCGCAAAGATCGGAAGA
++SOLEXA2_0414:3:1:13625:1097#0/1
+BJKJJTUUST___b_b_____b______________________________bW_bb__bb____[[Y[YYYYYY____BBBBBB
+@SOLEXA2_0414:3:1:14055:1098#0/1
+NAGCAATCTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCAGGACAA
++SOLEXA2_0414:3:1:14055:1098#0/1
+BMMMNWWWWWbbb________bb_______b_^__________bbb_________bb_b__b__b__b_bb____[Y[Y[VQWVV
+@SOLEXA2_0414:3:1:14195:1099#0/1
+NTGCGATCTCTGAATCTCCCGCAGTGTCCAATACTGTACTTTTTTACATAGTCATTGCTTAATGAATATGTATATCGCAAAGATC
++SOLEXA2_0414:3:1:14195:1099#0/1
+BPPPNVWVWV_b__bbb____bbb__bb__b_______b___bbQQ_b___bb_bb__b____b_b____b_bb___b____b__
+@SOLEXA2_0414:3:1:15892:1106#0/1
+NTGCGATAGACACATGAAGTTCCAAATTATTTTTTAACAATTTTTAAGGGAGACTGAGGCGAGAGAATCACTTGAGCCTGAGAGA
++SOLEXA2_0414:3:1:15892:1106#0/1
+BPOQMVWVVV_bbb_bb_b_b__________QQQQQbbb_b_b___b__b__________b____Z___________b_b____Z
+@SOLEXA2_0414:3:1:18397:1101#0/1
+NTGCGATATGGTTGATTATGTTTTTCTACATATTATTTGACATACTTCTATCTTCCCATGTTCTTACTATAGTTTGTGTATTGCC
++SOLEXA2_0414:3:1:18397:1101#0/1
+BHIKHWTRTTYYYYYXXVWWYYYQQOOOWWY[[[[__QQ_WWWTWXXXWW_______________YYYYYXXXXXWWWWWYYYYR
+@SOLEXA2_0414:3:1:4546:1111#0/1
+NCTACATCAAAAACATGCGTATGGACAAACCAGACCTTACAACTGTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGACAAAC
++SOLEXA2_0414:3:1:4546:1111#0/1
+BOIHKLRNMQXWWWQQ______________________________________________^_____________________Y
+@SOLEXA2_0414:3:1:5840:1112#0/1
+NTGCGATCTTAAAAATTGTTAAAAAATAATTTGGAACTTCATGTGTCTTTTGTATTGCTTGATAGCAGCATAGAATATGTGAGGT
++SOLEXA2_0414:3:1:5840:1112#0/1
+BQKKJRQONNKRNNL__________QQQQQVVVTTSSRSSQYYYYYYYYYQQQQ______BBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:6252:1110#0/1
+NTGCGATTACTCTGAATCTCCCGCAGTGTCCAATACTGTACTTTTTTACATAGTCATTGCTTAATGAATATGTATTGAATTAAAT
++SOLEXA2_0414:3:1:6252:1110#0/1
+BKIKHNRROR_b____b_____________________b___bbb_QQ_______________Q_YYYYY___T________W__
+@SOLEXA2_0414:3:1:6533:1111#0/1
+NCTACATGAGGGCGCTCGTTCTCCTCTAAACAAAACTTGTGGAAGGGCTCACAACAGACTTGGCAATACACAAACTATAGTAAGA
++SOLEXA2_0414:3:1:6533:1111#0/1
+BPPPPWWVVV____bb_bbbbbb_bbb____bQQQQ_b___b_b_____bb_bb____b_bb__b_bbbbb__b___________
+@SOLEXA2_0414:3:1:7569:1113#0/1
+NAGCAATTCTAAACAAAACTTGTGGAAGGGCTCACAACAGACTTGGCAATACACAAACTATAGTAAGAACATGGGAAGATAGAAG
++SOLEXA2_0414:3:1:7569:1113#0/1
+BIKOOPTTTT_____QQQQ_YYYYYYYYYY_____YYYYY___________________________________YQYYY___Y_
+@SOLEXA2_0414:3:1:7605:1117#0/1
+NAGCAATCCTTTAGTTCTAGTGTCTAGGGATATGCAAAGTCAGAAAAAACCAGTCACCACCCAAAAGAAAATAGTGCAGACAAGG
++SOLEXA2_0414:3:1:7605:1117#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:13482:1108#0/1
+NCTACATCTGAATCTCCCGCAGTGTCCGAGATCGCACCACTGCACCCCAGCCTGGGCGACAGCGAGACTCCGTCTCAAAAAAATA
++SOLEXA2_0414:3:1:13482:1108#0/1
+BLLLQVWWWVbb__bb___b_____b_____bb_b____________QQ_bbb_bY____OTVVOYVYYYVVSTTWWTTWYQQQQ
+@SOLEXA2_0414:3:1:14990:1109#0/1
+NTGCGATCTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTAACAGTTGTAAGGCCTGGTTTGTCCTGGACACTGCG
++SOLEXA2_0414:3:1:14990:1109#0/1
+BIGGJNRPOOYYYYYVWXWV_____YYRPWYYYYYXWWRWYYYYYVVTVTXXVWX_________Y[Y[[[_____YYYYY_____
+@SOLEXA2_0414:3:1:15871:1113#0/1
+NTGCGATATTTTTAAGGGAGACTGAGGCGAGAGAATCACTTGAGCCTGAGAGATCATGAGGACTCTTATAGGCCATGCTAAGACG
++SOLEXA2_0414:3:1:15871:1113#0/1
+BJJOHRTRTT[QQQ[___b____b______[V[[[bbbbb_b___b_b_____________________________________
+@SOLEXA2_0414:3:1:17840:1114#0/1
+NAGCAATCTCTAGATTACTTATCATACCTAATACAATGTAAATAGTTGTTATACTGTATTGTTTAGGAAATAATGACAAGAAAAA
++SOLEXA2_0414:3:1:17840:1114#0/1
+BOIIIVWWVV_____Y[[[[[[[W[TWTWRYYYYYY[YYY____R_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:18083:1109#0/1
+NAGCAATTACTCTGAATCTCCCGCAGTGTCCAATACTGTACTTTTTTACATAGTCATTGCTTAATGAATATGTATTGAATTAAAT
++SOLEXA2_0414:3:1:18083:1109#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:3606:1121#0/1
+NTGCGATGCATTAATTGTGTCTTTAAGGGTTAAACAGAGGCTCACAACAGACTTGACAATACACAAACTATAGTAAGAACATGGG
++SOLEXA2_0414:3:1:3606:1121#0/1
+BIIKHQTTSS[[[Y[_____YYYYYTWVVV_____b___^_________________________YYYYY_____BBBBBBBBBB
+@SOLEXA2_0414:3:1:4029:1119#0/1
+NAGCAATGGGAGAGTGTTGTTTTTGTCACTTGCCCCAGCAGAGCAGGGGTTTTGGAAGGAGAGGTCTTTAATAGCTTTGAAAATT
++SOLEXA2_0414:3:1:4029:1119#0/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:10939:1119#0/1
+NCTACATACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTATGTAGCAGATCGGGAGAGCGGTTCAGCAGGAAGGC
++SOLEXA2_0414:3:1:10939:1119#0/1
+BQKQLVWVWV_____[Y[[[__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:11098:1122#0/1
+NAGCAATGTTGAGTCCAGGGATACAGAACCCACTGATACAGAGGCCCAGCTGTAGTTCTATTACCAAGTTTTGTACCTTTGTAGC
++SOLEXA2_0414:3:1:11098:1122#0/1
+BEMGGQQORMVVVVTWWWWWOVTVVWRWWW_______________[[T[YTVTTV_____BBBBBBBBBBBBBBBBBBBBBBBBB
+@SOLEXA2_0414:3:1:12110:1126#0/1
+NTGCGATTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCAGATCGCAAAGATCGGAAGAGCGGTTCAGCAGGAATGCCG
++SOLEXA2_0414:3:1:12110:1126#0/1
+BIIIHQRRRQ[[[[[b__bb_b___YYYYY_____UWWWT[T[[Y__bb_________Y______YYYYYQWWWW___S_BBBBB