details: http://www.bx.psu.edu/hg/galaxy/rev/be8f54671d56 changeset: 3240:be8f54671d56 user: Anton Nekrutenko anton@bx.psu.edu date: Thu Jan 14 14:07:05 2010 -0500 description: Modification of pileup filter behavior, bases not different from the references are included in the report as well. Also changed the image for closing screencast panels. A new icon is urgently needed.
diffstat:
static/scripts/galaxy.panels.js | 2 +- static/welcome.html | 158 ++- test-data/pileup_parser.10col.20-3-yes-yes.pileup.out | 162 +- test-data/pileup_parser.6col.20-3-no-no.pileup.out | 1174 ++++++++-------- test-data/pileup_parser.6col.20-3-yes-no.pileup.out | 2 +- test-data/pileup_parser.6col.20-3-yes-yes.pileup.out | 2 +- tools/samtools/pileup_parser.pl | 4 +- tools/samtools/pileup_parser.xml | 6 +- 8 files changed, 822 insertions(+), 688 deletions(-)
diffs (1586 lines):
diff -r 517bd810a6b2 -r be8f54671d56 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Thu Jan 14 11:26:08 2010 -0500 +++ b/static/scripts/galaxy.panels.js Thu Jan 14 14:07:05 2010 -0500 @@ -210,7 +210,7 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:3px;top:3px;' src='../images/icon_error_sml.gif'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-12px;top:-12px;' src='../images/delete_icon.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); $("#close_button").bind( "click", function() { hide_modal() } ); }
diff -r 517bd810a6b2 -r be8f54671d56 static/welcome.html --- a/static/welcome.html Thu Jan 14 11:26:08 2010 -0500 +++ b/static/welcome.html Thu Jan 14 14:07:05 2010 -0500 @@ -2,20 +2,152 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link rel="stylesheet" href="style/base.css" type="text/css" /> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> +<link rel="stylesheet" href="style/base.css" type="text/css" /> +<style type="text/css"> + + .quickie { + text-align: center; + background: black; + margin: 10px; + } + + .current-quickie { + width: 300px; + background: white; + margin: auto; + } + + .current-quickie img { + padding: 15px; + border: 1px solid #ccc; + margin: auto; + background-color: white; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + + .previous { + width: 100%; + overflow: auto; + border: solid #ccc 1px; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + .previous .quickie { + padding-top: 10px; + min-height: 90px; + min-width: 150px; + } + #screencasts { + max-width: 50em; + margin-left: auto; + margin-right: auto; + } + +</style> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> +<script type="text/javascript"> + +$(document).ready(function() { + $('.current-quickie').cycle({ + fx: 'fade', + pause: 1, + speed: 100 + }); +}); +</script> </head> <body> - <div class="document"> - <div class="warningmessagelarge"> - <strong>Hello world! It's running...</strong> - <hr> - To customize this page edit <code>static/welcome.html</code> - </div> - <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> - <hr/> - This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. - </div> +<div class="document"> +<h3 align="center">Galaxy in 2010...</h3> +<div align="center" class="current-quickie"> + <a target="_blank" href="http://galaxy.psu.edu/dev2010/"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"/></a> + <a target="_blank" href="http://www.iscb.org/ismb2010"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /></a> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> + <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> +</div> +<br> +<hr> + +<h3 align="center">Galaxy Quickies</h3> + +<div class="previous" id="previous"> + <table border="0" cellpadding="0" cellspacing="0" width="100%"> + <tr> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie1_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie2_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie3_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie4_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie5_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie6_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie7_small.png" border="0"> + </div> + </a> + </td> + </tr> + </table> +</div> + +<script type="text/javascript"> + // Scroll to last quickie in box + document.getElementById("previous").scrollLeft = 100000000; +</script> + +<br/> +<br/> +<br/> +<hr/> + +<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> + +This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. +<p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> +</div> +</div> </body> </html> diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out --- a/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,86 +1,86 @@ -chrM 13 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII 0 0 1 0 17 -chrM 18 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A 0 0 1 0 19 -chrM 35 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII 0 0 1 0 28 -chrM 58 59 A A 50 0 24 16 ...............C IB20III:<DIII#II 0 1 0 0 13 -chrM 59 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI 1 0 0 0 16 +chrM 13 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII 16 0 1 0 17 +chrM 18 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A 0 0 1 18 19 +chrM 35 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII 27 0 1 0 28 +chrM 58 59 A A 50 0 24 16 ...............C IB20III:<DIII#II 12 1 0 0 13 +chrM 59 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI 1 15 0 0 16 chrM 157 158 A G 117 117 19 62 GGGGGGGGGGGGGGGGGGGNNNGGGGGG.GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGg^:g II6IIII<4I+IIIIIIII"""IIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII> 0 0 56 0 56 -chrM 170 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 0 0 1 0 46 -chrM 172 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII 0 1 0 0 37 -chrM 173 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII 0 1 0 0 39 -chrM 187 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII 0 0 1 0 12 -chrM 195 196 T T 17 0 19 5 G.... <IIII 0 0 1 0 5 -chrM 284 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII 0 0 0 1 11 -chrM 285 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II 1 0 0 0 8 -chrM 303 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* 1 0 0 0 12 -chrM 310 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* 0 1 0 0 12 -chrM 347 348 T T 4 0 20 3 ,$.$A IIA 1 0 0 0 3 -chrM 354 355 A C 14 36 25 4 .ccc IIII 0 3 0 0 4 +chrM 170 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 0 0 1 45 46 +chrM 172 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII 36 1 0 0 37 +chrM 173 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII 38 1 0 0 39 +chrM 187 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII 11 0 1 0 12 +chrM 195 196 T T 17 0 19 5 G.... <IIII 0 0 1 4 5 +chrM 284 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII 0 0 10 1 11 +chrM 285 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II 1 0 0 7 8 +chrM 303 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* 1 0 11 0 12 +chrM 310 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* 0 1 0 11 12 +chrM 347 348 T T 4 0 20 3 ,$.$A IIA 1 0 0 2 3 +chrM 354 355 A C 14 36 25 4 .ccc IIII 1 3 0 0 4 chrM 355 356 T C 39 39 25 4 Cccc IIII 0 4 0 0 4 chrM 380 381 C T 77 108 25 28 tttttttTttttgttttttttttt^:t^:t^:t^:t IIIIIIIIIIII&I7CI>BCA296+IA1 0 0 0 24 24 -chrM 383 384 A A 76 0 25 30 ,,,,,,,.,c,,g,,,,,,,g,,,,,,g,. IIIIIIIIIIII$IIIIIII$IIIIF,4II 0 1 0 0 26 +chrM 383 384 A A 76 0 25 30 ,,,,,,,.,c,,g,,,,,,,g,,,,,,g,. IIIIIIIIIIII$IIIIIII$IIIIF,4II 25 1 0 0 26 chrM 385 386 A G 88 120 25 32 gggggggGggnggggggggggggggggggGgg III>IIIIII"I&IIIIIIIIIIII?IIDI94 0 0 29 0 29 chrM 414 415 C T 75 75 25 16 t$t$tttttTttttTTTT IIIIIII>II93IIII 0 0 0 15 15 -chrM 464 465 C C 169 0 25 65 ,.............,,.....A.,......,..............,,,..........,a...,^:A IIIIBI>H1IIIIB$)IIIII$IIIIIIIIII0IIIII6IIIIIIHIIIIIIIIIIIII&IIICI 1 0 0 0 59 -chrM 468 469 T T 207 0 25 66 .$.$.$.........,,.......,......,..............,n,..........,,...,G... III>I44EIIICI@IIEDC$IBIIII(IIIIDIIII@IIIIII1"0IIII%IIIIII1III7IIII 0 0 1 0 57 -chrM 471 472 C C 187 0 25 72 .$.$.....,t.......,....A.,..............,a,..........,a...,A.......,,^:.^:.^:.^:.^:. I@IIIIII&IIIFG6IIIIII$IIIIIIIII$IIFIIII:IIIIIIIIIIII%IIII,IIIIII/I-IIIII 1 0 0 0 65 -chrM 490 491 C C 212 0 23 79 ..n,,....A.....,,...,........t,.....,....,..........,....,.,,...,.....,,..,.,., II"IIIIII&II:IIIIIIII(II@HIII;IIIIIIIIIIIIIIIIII?IIIIIIIIIIFIIIIIIIIIII+IIII3II 0 0 0 1 74 -chrM 506 507 A A 150 0 21 76 .$.$.$.$C$,....,..........c....,.,,...,.....,,..,.,.,,,,...,,,..,,....,,.,....^:.^:,^:, /I:3&I33.;I,./<G=I?IIIAIIIIIIIDI*IIIIIIIIIIIHDIIIIIIII=DIIIICIIII@IIIIII(I@6 0 1 0 0 65 -chrM 510 511 C C 213 0 21 72 .$.$.$....,....,.,,...,.....,,..,.,.,,,,...,,,..,,....,,.,...A.,,..,,,,,,,^:, III@/IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHIIIIIICIIEII6II/562I 1 0 0 0 69 -chrM 526 527 A A 164 0 22 58 ,,,...,,,..,,....,,.,.....,,..,,,,,,,,,..,,,..C,,,,,.,,,,, III3I=III;/II7I24II3I'II9IIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 1 0 0 52 -chrM 527 528 A A 164 0 22 58 g$,$,...,,,..,,....,,.,.....,,..,,,,,,,,,..,,,...,,,,,.,,,,, IIIF$9IIIIIII0A6(II4I+FI%:II4=IIIII'IIIIIIIIIIIIIIII3IIIII 0 0 1 0 49 -chrM 536 537 A A 138 0 23 49 .c,.,.....,,..,,,,,,,,,..,,,...,,,,,.,,,,,.,,,,,, 7II+I$0I8III/@IIIIIIIIIIIIIIIIIIIIIIIIIIIIII4I46I 0 1 0 0 43 -chrM 557 558 T T 83 0 23 27 ,$,$,$.,,,,,.,,,,,,.,.,....G.^:. 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"IC:6,1III=CIIIIB6GIII7G<DI>IIIIII8IIII$IHIII=I&IIIIIIIIIIIIIIIIIIIIIIII39IIIIIIIII 0 1 0 0 77 -chrM 763 764 G G 107 0 25 86 .$.$.$.$.$.$.$.$T$.....NN......................................AN...........................^:.^:.^:. 9I9I@8I4-I7IC&""=&=I+II=>I>IIIIIIIIIIIII@IIII+IIIIIIIII"II%IIIII@IIIIIIIIIIIIIIIIIIIII 1 0 0 0 76 -chrM 764 765 G G 88 0 25 77 .$.$.$.$.$.T..T.T............................................N.................... :,I;&I7D.%I'III<HD7IIIII*CIIIIIIIIII%IIIIIIIIIIIIIIIHIII"IIIIIIIIIIIIIIIIIIII 0 0 0 1 69 -chrM 767 768 T T 102 0 25 71 .$.$................................A.................................... &IBGII@5ICF>0?BII2IIIIII@+II;IEIII7I,III8IIIIIIIIIIIE@IIIIIIII8IIIIIIII 1 0 0 0 66 -chrM 777 778 G G 108 0 25 63 .$.$...T.....C......T...................T.......................^:. AG(II$IIIII&6BIII:'IIIII9IIIII=IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0 0 1 59 -chrM 784 785 A A 99 0 25 63 .$.........................................................C...^:. 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IHEF8II?+GI:I@I7%IIIIAIIII+IIA'II>II@IIIIIII3IIIII/III7IIIII5IIIIIIIIIIIIII+IIIIIIIIIIIIIIIAI6IIIIII;I8IIIIIIIIIIFIIIIIIIIIIIIIIIIIIIII""IIIAIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0 1 0 160 -chrM 816 817 A A 254 0 22 171 .$.C.......T..Nn..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,n,N,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,.^:.^!. 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IIIIIIIIIIII:IIIII%II5IIIIIIIIII?0B1I<IIGI)II1IDII*IIIIIIII)&III&I4>%5*II4(I 1 0 0 0 62 -chrM 951 952 A A 223 0 24 81 c.,,,,,,,,,,,,,,,c,,.,,,.,,,,,,,,,,,,,,,.,..,.,..,........,,,.,,.,,,,,..,,.^:.^:.^:.^:,^:,^:, IBIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIII8IIIIIIIIIIIIIIIIIIIIICIIII4IGIIIIIIIIIIIIII? 0 2 0 0 80 -chrM 952 953 C C 179 0 24 86 ,.,,,,,,,,,,,,,,,,,,.n,,.,,a,,,,,,a,,,,,.,..,.,..,........a,,.,,.,,,,,..,a....,,a^:.^!.^!.^:a^:a IIIIIIIIIIIIIIIIIIIII"IIIII)III6I1)I4II(I7II?I9II(IIIIIIII+1III0I+214%II79IIIIBB0III%I 2 0 0 0 69 -chrM 956 957 T T 237 0 23 110 ,.,,,,,,,,,,,,,,,,,,N,,,N,,,,,,,,,,,,,,,G,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,NN,^:.^:,^:,^:,^:.^:.^:. 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III+IIIIIII>IHDIG4I4IIIIIII 0 0 1 23 24 +chrM 606 607 G G 105 0 24 43 ..............,....T..T..................^:.^!, BI-&*1&6IIIGIIII%;9I.;>IIIIIIIIIIIIIIIIIII3 0 0 33 2 35 +chrM 618 619 T T 117 0 24 48 ,.........C..C..............,...........N..,...^:. I2&-+)(4I+>CI$&I15@IIIIIIIII,IIIIIIIIIII"II5IIII 0 1 0 34 35 +chrM 627 628 G G 108 0 22 57 .$...........A........,..............,................A^!.^!.^:. 5GI<=4;>G=I<%IIIIII.IIII'IIIIIIII$IIIIIIIIIIIIIIIIIIIIIII 1 0 51 0 52 +chrM 659 660 C C 166 0 19 58 .$.$.............,...n,.,,......,......................a,... /CII>9@II277IIII9II"IIIIIIFIIIIIIBIIIIIIIIIIIIIIII$II7IIII 1 53 0 0 54 +chrM 668 669 C C 135 0 19 42 .$,$,$......,.....................Ga,......,^:. IIIIIII@IIFI@IIIIIIIII;IIIIHIII56IIIIIIIAI 1 40 1 0 42 +chrM 713 714 A A 127 0 23 96 ...,..C.....................,......................,............................C...........^:.^:.^:.^:. 67'II>(IIIAFI<IIIII?I$EI>GAGII4III8IIDIIIDIIIFIIIIG$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 90 1 0 0 91 +chrM 719 720 T T 130 0 24 96 .....C...........,...C.....G............,............G....................A...................^:.^:. D?76/$I'@'<,I7;I<I5GI'H+B.3%;=<3II1CGIIB@FII8@II0II4II$IIIII537IIIIIIIIIII#IIIIIIIII=III$IIIIIII 0 0 1 77 78 +chrM 736 737 A A 98 0 24 98 .$.$.$..............................C................T.......................C..................^:.^:.^:.^:.^:. 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III 0 0 0 0 3 -chrM 317 C 3 ,.. III 0 0 0 0 3 -chrM 318 C 3 ,.. III 0 0 0 0 3 -chrM 319 A 3 ,$.. III 0 0 0 0 3 -chrM 390 A 3 ..^:. III 0 0 0 0 3 -chrM 391 A 3 ... >II 0 0 0 0 3 -chrM 392 A 3 ... III 0 0 0 0 3 -chrM 393 T 3 ... III 0 0 0 0 3 -chrM 394 A 3 ... III 0 0 0 0 3 -chrM 395 A 3 .$.. III 0 0 0 0 3 -chrM 400 A 3 ..^:. III 0 0 0 0 3 -chrM 401 A 3 ... III 0 0 0 0 3 -chrM 402 A 3 ... III 0 0 0 0 3 -chrM 403 A 3 ... III 0 0 0 0 3 -chrM 404 C 3 ... III 0 0 0 0 3 -chrM 405 C 3 ... III 0 0 0 0 3 -chrM 406 C 3 ... EII 0 0 0 0 3 -chrM 407 A 3 ... III 0 0 0 0 3 -chrM 408 G 3 ... III 0 0 0 0 3 -chrM 409 T 3 ... 0II 0 0 0 0 2 -chrM 410 T 3 ... III 0 0 0 0 3 -chrM 411 A 4 ...^:, IIII 0 0 0 0 4 -chrM 412 A 4 ..., FIII 0 0 0 0 4 -chrM 413 G 4 ..., IIIH 0 0 0 0 4 -chrM 414 C 4 ...a III2 0 0 0 0 3 +chrM 45 A 3 ..^:. III 3 0 0 0 3 +chrM 46 G 4 ...^:. IIII 0 0 4 0 4 +chrM 47 A 5 ....^:, IIIII 5 0 0 0 5 +chrM 48 T 5 ...., IIIII 0 0 0 5 5 +chrM 49 G 5 ...., IIIII 0 0 5 0 5 +chrM 50 A 5 ...., IIIII 5 0 0 0 5 +chrM 51 G 5 ...., IIIII 0 0 5 0 5 +chrM 52 T 5 ...., IIIII 0 0 0 5 5 +chrM 53 A 5 ...., IIIII 5 0 0 0 5 +chrM 54 T 5 ...., IIIII 0 0 0 5 5 +chrM 55 T 5 ...., IIIII 0 0 0 5 5 +chrM 56 C 5 ...., IIIII 0 5 0 0 5 +chrM 57 T 5 ...., IIIII 0 0 0 5 5 +chrM 58 T 5 ...., IIIII 0 0 0 5 5 +chrM 59 A 5 ...., IIIII 5 0 0 0 5 +chrM 60 C 5 ...., IIIII 0 5 0 0 5 +chrM 61 T 5 ...., IIIII 0 0 0 5 5 +chrM 62 C 5 ...., IIIII 0 5 0 0 5 +chrM 63 C 5 ...., IIIII 0 5 0 0 5 +chrM 64 A 5 ...., IIIII 5 0 0 0 5 +chrM 65 T 5 ...., IIIII 0 0 0 5 5 +chrM 66 A 5 ...., IIIII 5 0 0 0 5 +chrM 67 A 5 ...., IIIII 5 0 0 0 5 +chrM 68 A 5 ...., IIICI 5 0 0 0 5 +chrM 69 C 5 ...., IIIII 0 5 0 0 5 +chrM 70 A 5 ...., IIIII 5 0 0 0 5 +chrM 71 C 5 ...., IIIII 0 5 0 0 5 +chrM 72 A 5 ...., IAIII 5 0 0 0 5 +chrM 73 T 5 ...., IIIII 0 0 0 5 5 +chrM 74 A 5 ...., IIIII 5 0 0 0 5 +chrM 75 G 5 ...., %IIII 0 0 4 0 4 +chrM 76 G 5 T..., *IIII 0 0 4 0 4 +chrM 77 C 5 .$..., GIIII 0 5 0 0 5 +chrM 78 T 4 .$.., IIII 0 0 0 4 4 +chrM 79 T 3 .., III 0 0 0 3 3 +chrM 80 G 3 .$., I1I 0 0 2 0 2 +chrM 181 A 3 ,,^:, III 3 0 0 0 3 +chrM 182 G 3 ,,, III 0 0 3 0 3 +chrM 183 G 3 ,,, III 0 0 3 0 3 +chrM 184 T 3 ,,, III 0 0 0 3 3 +chrM 185 A 3 ,,, III 3 0 0 0 3 +chrM 186 T 3 ,,, III 0 0 0 3 3 +chrM 187 C 3 ,,, III 0 3 0 0 3 +chrM 188 A 3 ,,, III 3 0 0 0 3 +chrM 189 A 3 ,,, III 3 0 0 0 3 +chrM 190 G 3 ,,, III 0 0 3 0 3 +chrM 191 C 3 ,$,, III 0 3 0 0 3 +chrM 229 A 3 .^:,^:, %II 2 0 0 0 2 +chrM 230 C 3 .,, 8II 0 3 0 0 3 +chrM 231 C 3 .,, 9II 0 3 0 0 3 +chrM 232 C 3 .,, III 0 3 0 0 3 +chrM 233 C 3 .,, AI' 0 2 0 0 2 +chrM 234 C 3 .,, DI+ 0 2 0 0 2 +chrM 235 A 3 .,, &I@ 2 0 0 0 2 +chrM 236 C 3 .$,a +I$ 0 1 0 0 1 +chrM 244 A 3 ,,^:, II; 3 0 0 0 3 +chrM 245 G 3 ,,, II* 0 0 2 0 2 +chrM 246 C 3 ,,n II" 0 2 0 0 2 +chrM 247 A 3 ,,, III 3 0 0 0 3 +chrM 248 G 4 ,,,^:. IIII 0 0 4 0 4 +chrM 249 T 4 ,,,. II)I 0 0 0 3 3 +chrM 250 G 4 ,,,. II2I 0 0 3 0 3 +chrM 251 A 4 ,,,. II(I 3 0 0 0 3 +chrM 252 T 4 ,,,. II*I 0 0 0 3 3 +chrM 253 A 4 ,,,. II7I 4 0 0 0 4 +chrM 254 A 4 ,,,. II1I 3 0 0 0 3 +chrM 255 A 4 ,,,. II?I 4 0 0 0 4 +chrM 256 A 4 ,,,. II9I 4 0 0 0 4 +chrM 257 A 4 ,,,. II?I 4 0 0 0 4 +chrM 258 T 4 ,,,. II$I 0 0 0 3 3 +chrM 259 T 5 ,,,.^:. II&II 0 0 0 4 4 +chrM 260 A 5 ,,,.. II,II 4 0 0 0 4 +chrM 261 A 5 ,,,.. II/II 4 0 0 0 4 +chrM 262 G 5 ,,,.. II5II 0 0 5 0 5 +chrM 263 C 5 ,,a.. II%II 0 4 0 0 4 +chrM 264 T 5 ,$,$,.. II%II 0 0 0 4 4 +chrM 265 A 3 ,.. )II 2 0 0 0 2 +chrM 266 T 3 ,.. +II 0 0 0 2 2 +chrM 267 G 4 ,..^:. *III 0 0 3 0 3 +chrM 268 A 4 ,... EIII 4 0 0 0 4 +chrM 269 A 4 ,... =III 4 0 0 0 4 +chrM 270 C 4 a... ;III 1 3 0 0 4 +chrM 271 G 4 ,... ;III 0 0 4 0 4 +chrM 272 A 4 ,... 8@II 4 0 0 0 4 +chrM 273 A 4 ,... 1III 3 0 0 0 3 +chrM 274 A 4 ,... ICII 4 0 0 0 4 +chrM 275 G 4 ,... IIII 0 0 4 0 4 +chrM 276 T 4 ,... IIII 0 0 0 4 4 +chrM 277 T 4 ,... IIII 0 0 0 4 4 +chrM 278 C 4 ,... IIII 0 4 0 0 4 +chrM 279 G 4 ,$... IIII 0 0 4 0 4 +chrM 280 A 3 ... III 3 0 0 0 3 +chrM 281 C 3 ... GII 0 3 0 0 3 +chrM 282 T 3 ... III 0 0 0 3 3 +chrM 283 A 3 .$.. IFI 3 0 0 0 3 +chrM 284 A 3 ..^:, IAI 3 0 0 0 3 +chrM 285 G 3 .., ;II 0 0 3 0 3 +chrM 286 T 4 ..,^:. IIII 0 0 0 4 4 +chrM 287 C 4 ..,. II4I 0 3 0 0 3 +chrM 288 A 4 ..,. @III 4 0 0 0 4 +chrM 289 T 4 ..,. IIII 0 0 0 4 4 +chrM 290 A 4 ..,. @:II 4 0 0 0 4 +chrM 291 T 4 ..,. IIAI 0 0 0 4 4 +chrM 292 T 4 ..,. IIII 0 0 0 4 4 +chrM 293 A 4 ..,. 8;II 4 0 0 0 4 +chrM 294 A 4 .$.,. I<II 4 0 0 0 4 +chrM 295 A 3 .,. 4II 2 0 0 0 2 +chrM 296 T 3 .,. III 0 0 0 3 3 +chrM 297 A 3 .,. BII 3 0 0 0 3 +chrM 298 A 3 .,. CII 3 0 0 0 3 +chrM 299 G 3 .,. III 0 0 3 0 3 +chrM 300 G 3 .,. ;II 0 0 3 0 3 +chrM 301 G 3 .,. III 0 0 3 0 3 +chrM 302 T 3 .$,. III 0 0 0 3 3 +chrM 312 T 3 ,.^:. III 0 0 0 3 3 +chrM 313 C 3 ,.. III 0 3 0 0 3 +chrM 314 G 3 ,.. III 0 0 3 0 3 +chrM 315 T 3 ,.. III 0 0 0 3 3 +chrM 316 G 3 ,.. III 0 0 3 0 3 +chrM 317 C 3 ,.. III 0 3 0 0 3 +chrM 318 C 3 ,.. III 0 3 0 0 3 +chrM 319 A 3 ,$.. III 3 0 0 0 3 +chrM 390 A 3 ..^:. III 3 0 0 0 3 +chrM 391 A 3 ... >II 3 0 0 0 3 +chrM 392 A 3 ... III 3 0 0 0 3 +chrM 393 T 3 ... III 0 0 0 3 3 +chrM 394 A 3 ... III 3 0 0 0 3 +chrM 395 A 3 .$.. III 3 0 0 0 3 +chrM 400 A 3 ..^:. III 3 0 0 0 3 +chrM 401 A 3 ... III 3 0 0 0 3 +chrM 402 A 3 ... III 3 0 0 0 3 +chrM 403 A 3 ... III 3 0 0 0 3 +chrM 404 C 3 ... III 0 3 0 0 3 +chrM 405 C 3 ... III 0 3 0 0 3 +chrM 406 C 3 ... EII 0 3 0 0 3 +chrM 407 A 3 ... III 3 0 0 0 3 +chrM 408 G 3 ... III 0 0 3 0 3 +chrM 409 T 3 ... 0II 0 0 0 2 2 +chrM 410 T 3 ... III 0 0 0 3 3 +chrM 411 A 4 ...^:, IIII 4 0 0 0 4 +chrM 412 A 4 ..., FIII 4 0 0 0 4 +chrM 413 G 4 ..., IIIH 0 0 4 0 4 +chrM 414 C 4 ...a III2 0 3 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 -chrM 416 G 5 ...,^:, II?7: 0 0 0 0 5 -chrM 417 T 5 ...,, ;IIE@ 0 0 0 0 5 -chrM 418 A 5 ...,, IIIII 0 0 0 0 5 -chrM 419 A 5 ...,, IIIII 0 0 0 0 5 -chrM 420 A 5 ...,, FIIII 0 0 0 0 5 -chrM 421 A 5 ...,, IIIII 0 0 0 0 5 -chrM 422 A 5 ...,, >IIII 0 0 0 0 5 -chrM 423 G 6 ...,,^:, HII/I, 0 0 0 0 4 -chrM 424 C 6 .$..a,, ;II-I: 0 0 0 0 5 -chrM 425 T 5 .$.,,, IIIIF 0 0 0 0 5 -chrM 426 A 5 .,,,^:, III@I 0 0 0 0 5 -chrM 427 C 5 .,,,, III$I 0 0 0 0 4 -chrM 428 A 5 .,,,, IIIII 0 0 0 0 5 -chrM 429 A 5 .,,,, IIII. 0 0 0 0 4 -chrM 430 C 5 .,,,a I%I5' 0 0 0 0 3 -chrM 431 C 5 .,,,, I(I5< 0 0 0 0 4 -chrM 432 A 5 .,,,, IIIII 0 0 0 0 5 -chrM 433 A 5 .,,,, 0IIII 0 0 0 0 4 -chrM 434 A 5 .,,,, =IIII 0 0 0 0 5 -chrM 435 G 5 .$,,,, EIIII 0 0 0 0 5 -chrM 436 T 4 ,,,, III5 0 0 0 0 4 -chrM 437 A 4 ,,,, IIII 0 0 0 0 4 -chrM 438 A 4 ,,,, IIII 0 0 0 0 4 -chrM 439 A 4 ,,,, IIII 0 0 0 0 4 -chrM 440 A 4 ,,,, IIIF 0 0 0 0 4 -chrM 441 T 6 ,,,,^:.^:. III;II 0 0 0 0 6 -chrM 442 A 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 443 G 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 444 A 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 445 C 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 446 T 6 ,$,,,.. IIIIII 0 0 0 0 6 -chrM 447 A 5 ,,,.. IIIII 0 0 0 0 5 -chrM 448 C 5 ,,,.. IIIII 0 0 0 0 5 -chrM 449 G 6 ,,,..^:, IIIII6 0 0 0 0 6 -chrM 450 A 6 ,,,.., IIIIII 0 0 0 0 6 -chrM 451 A 6 ,$,,.., IIIIII 0 0 0 0 6 -chrM 452 A 5 ,,.., IIIII 0 0 0 0 5 -chrM 453 G 5 ,,.., IIIII 0 0 0 0 5 -chrM 454 T 6 ,,..,^:, IIIIII 0 0 0 0 6 -chrM 455 G 6 ,,..,, IIIIII 0 0 0 0 6 -chrM 456 A 6 ,,..,, IIIIII 0 0 0 0 6 -chrM 457 C 6 ,,..,, IIIII= 0 0 0 0 6 -chrM 458 T 6 ,$,..,, IIIIII 0 0 0 0 6 -chrM 459 T 5 ,..,, IIIII 0 0 0 0 5 -chrM 460 T 5 ,..,, IIIII 0 0 0 0 5 -chrM 461 A 5 ,$..,, IIIII 0 0 0 0 5 -chrM 462 A 4 ..,, IIII 0 0 0 0 4 -chrM 463 T 4 ..,, IIIC 0 0 0 0 4 -chrM 464 A 4 ..,, IIII 0 0 0 0 4 -chrM 465 C 4 ..,, IIII 0 0 0 0 4 -chrM 466 C 4 ..,, IIII 0 0 0 0 4 -chrM 467 T 4 ..,, II>? 0 0 0 0 4 -chrM 468 C 4 ..,, IIII 0 0 0 0 4 -chrM 469 T 4 ..,, IIIG 0 0 0 0 4 -chrM 470 G 4 ..,, %III 0 0 0 0 3 -chrM 471 A 4 ..,, 4;II 0 0 0 0 3 -chrM 472 C 4 ..,, II3I 0 0 0 0 3 -chrM 473 T 4 ..,, IIII 0 0 0 0 4 -chrM 474 A 4 ..,, ;III 0 0 0 0 4 -chrM 475 C 4 ..,, IIII 0 0 0 0 4 -chrM 476 A 4 .$.$,, 32II 0 0 0 0 2 -chrM 480 T 3 ,,^:. III 0 0 0 0 3 -chrM 481 A 3 ,,. III 0 0 0 0 3 -chrM 482 G 3 ,,. III 0 0 0 0 3 -chrM 483 C 4 ,,.^:, IIIE 0 0 0 0 4 -chrM 484 T 4 ,$,., III9 0 0 0 0 4 -chrM 485 A 3 ,., III 0 0 0 0 3 -chrM 486 A 3 ,., III 0 0 0 0 3 -chrM 487 G 3 ,., III 0 0 0 0 3 -chrM 488 A 3 ,., III 0 0 0 0 3 -chrM 489 C 3 ,$., III 0 0 0 0 3 -chrM 510 C 3 .,^:. III 0 0 0 0 3 -chrM 511 C 3 .,. III 0 0 0 0 3 -chrM 512 A 3 .,. 6II 0 0 0 0 3 -chrM 513 C 3 .,. III 0 0 0 0 3 -chrM 514 T 3 .,. III 0 0 0 0 3 -chrM 515 A 3 .$,. III 0 0 0 0 3 -chrM 518 C 3 ,$.^:. III 0 0 0 0 3 -chrM 520 T 3 ..^:, III 0 0 0 0 3 -chrM 521 A 3 .., III 0 0 0 0 3 -chrM 522 G 3 .., II, 0 0 0 0 2 -chrM 523 C 3 .., III 0 0 0 0 3 -chrM 524 C 3 .., II7 0 0 0 0 3 -chrM 525 C 3 .., III 0 0 0 0 3 -chrM 526 T 3 .., II? 0 0 0 0 3 -chrM 527 A 3 .., III 0 0 0 0 3 -chrM 528 A 3 .., III 0 0 0 0 3 -chrM 529 A 3 .., FII 0 0 0 0 3 -chrM 530 C 3 .., II+ 0 0 0 0 2 -chrM 531 T 3 .., III 0 0 0 0 3 -chrM 532 A 3 .., :II 0 0 0 0 3 -chrM 533 A 3 .., DGI 0 0 0 0 3 -chrM 534 A 3 .., III 0 0 0 0 3 -chrM 535 A 3 .., ?CI 0 0 0 0 3 -chrM 536 T 3 .., III 0 0 0 0 3 -chrM 537 A 3 .., 9II 0 0 0 0 3 -chrM 538 G 3 .., III 0 0 0 0 3 -chrM 539 C 3 .., III 0 0 0 0 3 -chrM 540 T 3 .., III 0 0 0 0 3 -chrM 541 T 3 .., III 0 0 0 0 3 -chrM 542 A 4 ..,^:. IIII 0 0 0 0 4 -chrM 543 C 4 ..,. IIII 0 0 0 0 4 -chrM 544 C 4 ..,. IIII 0 0 0 0 4 -chrM 545 A 4 N$.,. "III 0 0 0 0 3 -chrM 546 C 3 .,. III 0 0 0 0 3 -chrM 547 A 3 .,. DII 0 0 0 0 3 -chrM 548 A 3 .,. EII 0 0 0 0 3 -chrM 549 C 3 .,. III 0 0 0 0 3 -chrM 550 A 3 .,. III 0 0 0 0 3 -chrM 551 A 3 .,. 6II 0 0 0 0 3 -chrM 552 A 3 .,. GII 0 0 0 0 3 -chrM 553 G 3 .$,. ?II 0 0 0 0 3 -chrM 577 A 3 .$.^:. III 0 0 0 0 3 -chrM 580 A 3 ..^:, III 0 0 0 0 3 -chrM 581 G 3 .., III 0 0 0 0 3 -chrM 582 C 3 .., II? 0 0 0 0 3 -chrM 583 C 3 ..a II- 0 0 0 0 2 -chrM 584 T 3 .., IIH 0 0 0 0 3 -chrM 585 A 3 .., III 0 0 0 0 3 -chrM 586 A 3 .., III 0 0 0 0 3 -chrM 587 A 4 ..,^:, IIII 0 0 0 0 4 -chrM 588 A 4 ..,, IIII 0 0 0 0 4 -chrM 589 C 4 ..,, IIII 0 0 0 0 4 -chrM 590 T 4 ..,, II.5 0 0 0 0 3 -chrM 591 C 4 .$.,, II<I 0 0 0 0 4 -chrM 592 A 3 .,, III 0 0 0 0 3 -chrM 593 A 3 .,, III 0 0 0 0 3 -chrM 594 A 3 .,, III 0 0 0 0 3 -chrM 595 G 3 .,, III 0 0 0 0 3 -chrM 596 G 3 .,, III 0 0 0 0 3 -chrM 597 A 3 .,, :EI 0 0 0 0 3 -chrM 598 C 3 .,, III 0 0 0 0 3 -chrM 599 T 4 .,,^:. II@I 0 0 0 0 4 -chrM 600 T 4 .,,. IIII 0 0 0 0 4 -chrM 601 G 4 .,,. IIII 0 0 0 0 4 -chrM 602 G 4 .,,. IIII 0 0 0 0 4 -chrM 603 C 4 .,,. IIII 0 0 0 0 4 -chrM 604 G 4 .,,. IIII 0 0 0 0 4 -chrM 605 G 4 .,,. IIII 0 0 0 0 4 -chrM 606 T 4 .,,. 5III 0 0 0 0 4 -chrM 607 G 4 .,,. IIII 0 0 0 0 4 -chrM 608 C 4 .,,. *III 0 0 0 0 3 -chrM 609 T 5 .,,.^:, ?IIII 0 0 0 0 5 -chrM 610 T 5 .,,., IIII8 0 0 0 0 5 -chrM 611 T 5 .,,., IIIII 0 0 0 0 5 -chrM 612 A 5 T$,,., 3IIII 0 0 0 0 4 -chrM 613 C 4 ,,., III) 0 0 0 0 3 -chrM 614 A 4 ,,., IIII 0 0 0 0 4 -chrM 615 T 4 ,$,., IIII 0 0 0 0 4 -chrM 616 C 3 ,., III 0 0 0 0 3 -chrM 617 C 3 ,., III 0 0 0 0 3 -chrM 618 C 3 ,., III 0 0 0 0 3 -chrM 619 T 3 ,., IF9 0 0 0 0 3 -chrM 620 C 3 ,., II7 0 0 0 0 3 -chrM 621 T 3 ,., III 0 0 0 0 3 -chrM 622 A 3 ,$., I7I 0 0 0 0 3 -chrM 652 C 3 .,^:, II) 0 0 0 0 2 -chrM 653 G 3 .,, II2 0 0 0 0 2 -chrM 654 A 3 .,, III 0 0 0 0 3 -chrM 655 T 4 .,,^:. II*I 0 0 0 0 3 -chrM 656 A 4 .,,. IIII 0 0 0 0 4 -chrM 657 A 4 .,,. IIII 0 0 0 0 4 -chrM 658 A 4 .,,. IIII 0 0 0 0 4 -chrM 659 C 4 .,,. IIII 0 0 0 0 4 -chrM 660 C 4 .,,. IIII 0 0 0 0 4 -chrM 661 C 4 .,,. IIII 0 0 0 0 4 -chrM 662 C 4 .,,. IIFI 0 0 0 0 4 -chrM 663 A 4 .,,. =IDI 0 0 0 0 4 -chrM 664 C 4 .,,. II6I 0 0 0 0 4 -chrM 665 C 5 .,,.^:, IIIII 0 0 0 0 5 -chrM 666 A 5 .,,., BIIII 0 0 0 0 5 -chrM 667 T 5 .,,., II5I+ 0 0 0 0 4 -chrM 668 C 5 .,,., IIIII 0 0 0 0 5 -chrM 669 C 5 .,,., IIIII 0 0 0 0 5 -chrM 670 C 5 .,a., II.II 0 0 0 0 4 -chrM 671 T 5 .,,., IIIIA 0 0 0 0 5 -chrM 672 T 6 .,,.,^:. FI9I.I 0 0 0 0 5 -chrM 673 G 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 674 C 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 675 T 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 676 A 6 .,,.,. ,IIEII 0 0 0 0 5 -chrM 677 A 7 .,,.,.^:. 3II;III 0 0 0 0 6 -chrM 678 T 7 .,,.,.. IIIIDII 0 0 0 0 7 -chrM 679 T 7 .,,.,.. CIIIIII 0 0 0 0 7 -chrM 680 C 7 .,,.,.. IIIIIII 0 0 0 0 7 -chrM 681 A 7 .$,,.,.. 9IIIIII 0 0 0 0 7 -chrM 682 G 6 ,,.,.. II$III 0 0 0 0 5 -chrM 683 C 6 ,,.,.. IIIIII 0 0 0 0 6 -chrM 684 C 6 ,$,.,.. IIIIII 0 0 0 0 6 -chrM 685 T 5 ,.,.. IIIII 0 0 0 0 5 -chrM 686 A 5 ,.,.. IIIII 0 0 0 0 5 -chrM 687 T 5 ,$.,.. IIIII 0 0 0 0 5 -chrM 688 A 4 .,.. IIII 0 0 0 0 4 -chrM 689 T 4 .,.. IIII 0 0 0 0 4 -chrM 690 A 4 .$,.. IIII 0 0 0 0 4 -chrM 691 C 3 ,.. III 0 0 0 0 3 -chrM 692 C 3 ,.. III 0 0 0 0 3 -chrM 693 G 4 ,..^:, IIII 0 0 0 0 4 -chrM 694 C 4 ,.., IIII 0 0 0 0 4 -chrM 695 C 4 ,.., IIII 0 0 0 0 4 -chrM 696 A 4 ,.., IIII 0 0 0 0 4 -chrM 697 T 4 ,.., IIII 0 0 0 0 4 -chrM 698 C 4 ,.., IIII 0 0 0 0 4 -chrM 699 T 4 ,.., IIII 0 0 0 0 4 -chrM 700 T 4 ,$.., IIII 0 0 0 0 4 -chrM 701 C 3 .., III 0 0 0 0 3 -chrM 702 A 3 .., III 0 0 0 0 3 -chrM 703 G 3 .., 2II 0 0 0 0 2 -chrM 704 C 3 .., III 0 0 0 0 3 -chrM 705 A 3 N., "II 0 0 0 0 2 -chrM 706 A 3 .., I5I 0 0 0 0 3 -chrM 707 A 3 .$., GII 0 0 0 0 3 -chrM 726 A 3 ,,^:. III 0 0 0 0 3 -chrM 727 G 3 ,,. III 0 0 0 0 3 -chrM 728 T 3 ,$,. III 0 0 0 0 3 -chrM 732 C 3 a.^:. $II 0 0 0 0 2 -chrM 733 A 3 ,.. III 0 0 0 0 3 -chrM 734 C 3 ,.. %II 0 0 0 0 2 -chrM 735 A 3 ,.. III 0 0 0 0 3 -chrM 736 A 3 ,.. *II 0 0 0 0 2 -chrM 737 A 3 ,.. III 0 0 0 0 3 -chrM 738 T 3 ,.. III 0 0 0 0 3 -chrM 739 A 3 ,.. III 0 0 0 0 3 -chrM 740 T 3 ,.. III 0 0 0 0 3 -chrM 741 C 3 ,.. III 0 0 0 0 3 -chrM 742 C 3 ,.. III 0 0 0 0 3 -chrM 743 A 3 ,.. III 0 0 0 0 3 -chrM 744 A 3 ,.. III 0 0 0 0 3 -chrM 745 C 3 ,.. III 0 0 0 0 3 -chrM 746 A 3 ,.. IIE 0 0 0 0 3 -chrM 747 T 3 ,.. III 0 0 0 0 3 -chrM 748 A 3 ,.. III 0 0 0 0 3 -chrM 749 A 3 ,.. III 0 0 0 0 3 -chrM 750 A 3 ,.. III 0 0 0 0 3 -chrM 751 A 3 ,.. IAI 0 0 0 0 3 -chrM 752 A 3 ,.. III 0 0 0 0 3 -chrM 753 C 3 ,.. III 0 0 0 0 3 -chrM 754 G 3 ,$.. III 0 0 0 0 3 -chrM 756 T 3 ..^:, III 0 0 0 0 3 -chrM 757 A 3 .., III 0 0 0 0 3 -chrM 758 G 3 .., III 0 0 0 0 3 -chrM 759 G 3 .., III 0 0 0 0 3 -chrM 760 T 3 .., =II 0 0 0 0 3 -chrM 761 C 3 .$., IID 0 0 0 0 3 -chrM 767 G 3 .$,^:, III 0 0 0 0 3 -chrM 769 A 3 ,,^:, III 0 0 0 0 3 -chrM 770 G 3 ,,, III 0 0 0 0 3 -chrM 771 C 3 ,,, IHI 0 0 0 0 3 -chrM 772 C 3 ,a, I)/ 0 0 0 0 1 -chrM 773 C 3 ,,, I7I 0 0 0 0 3 -chrM 774 A 4 ,,,^:. II:I 0 0 0 0 4 -chrM 775 T 4 ,,,. IH.I 0 0 0 0 3 -chrM 776 G 4 ,,,. IIII 0 0 0 0 4 -chrM 777 G 4 ,,,. IIII 0 0 0 0 4 -chrM 778 G 4 ,,,. IIII 0 0 0 0 4 -chrM 779 A 4 ,,,. IIAI 0 0 0 0 4 -chrM 780 T 4 ,,,. IIGI 0 0 0 0 4 -chrM 781 G 4 ,,,. IIII 0 0 0 0 4 -chrM 782 G 4 ,,,. IIII 0 0 0 0 4 -chrM 783 A 4 ,,,. IIII 0 0 0 0 4 -chrM 784 G 4 ,,,. IIII 0 0 0 0 4 -chrM 785 A 4 ,,,. IIII 0 0 0 0 4 -chrM 786 G 4 ,,,. IIII 0 0 0 0 4 -chrM 787 A 4 ,,,. IIII 0 0 0 0 4 -chrM 788 A 4 ,,,. IIII 0 0 0 0 4 -chrM 789 A 4 ,,,. IIII 0 0 0 0 4 -chrM 790 T 5 ,,,.^:. IIIII 0 0 0 0 5 -chrM 791 G 5 ,$,,.. IIIII 0 0 0 0 5 -chrM 792 G 4 ,,.. IIII 0 0 0 0 4 -chrM 793 G 4 ,,.. IIII 0 0 0 0 4 -chrM 794 C 4 ,,.. IIII 0 0 0 0 4 -chrM 795 T 4 ,,.. IIII 0 0 0 0 4 -chrM 796 A 4 ,,.. IIII 0 0 0 0 4 -chrM 797 C 4 ,,.. IIII 0 0 0 0 4 -chrM 798 A 4 ,,.. IIII 0 0 0 0 4 -chrM 799 T 4 ,,.. IIII 0 0 0 0 4 -chrM 800 T 4 ,,.. IIII 0 0 0 0 4 -chrM 801 T 4 ,,.. IIII 0 0 0 0 4 -chrM 802 T 4 ,$,.. IIII 0 0 0 0 4 -chrM 803 C 3 ,.. III 0 0 0 0 3 -chrM 804 T 3 ,$.. III 0 0 0 0 3 -chrM 806 C 3 ..^:. III 0 0 0 0 3 -chrM 807 C 3 ... III 0 0 0 0 3 -chrM 808 C 3 ... III 0 0 0 0 3 -chrM 809 T 3 .$.. III 0 0 0 0 3 -chrM 810 A 3 ..^:, III 0 0 0 0 3 -chrM 811 A 3 .., III 0 0 0 0 3 -chrM 812 G 3 .., II7 0 0 0 0 3 -chrM 813 A 3 .., III 0 0 0 0 3 -chrM 814 A 3 .., III 0 0 0 0 3 -chrM 815 C 3 .., III 0 0 0 0 3 -chrM 816 A 3 .., III 0 0 0 0 3 -chrM 817 A 3 .., III 0 0 0 0 3 -chrM 818 G 3 .., III 0 0 0 0 3 -chrM 819 A 3 .., III 0 0 0 0 3 -chrM 820 A 3 .., &II 0 0 0 0 2 -chrM 821 C 3 .., III 0 0 0 0 3 -chrM 822 T 3 .., III 0 0 0 0 3 -chrM 823 T 3 ..n II" 0 0 0 0 2 -chrM 824 T 3 .., III 0 0 0 0 3 -chrM 825 A 3 .$., III 0 0 0 0 3 -chrM 826 A 3 .,^:. III 0 0 0 0 3 -chrM 827 C 3 .,. III 0 0 0 0 3 -chrM 828 C 3 .,. III 0 0 0 0 3 -chrM 829 C 4 .,.^:, IIII 0 0 0 0 4 -chrM 830 G 4 .,., IIII 0 0 0 0 4 -chrM 831 G 4 .,., IIII 0 0 0 0 4 -chrM 832 A 4 .,., IIII 0 0 0 0 4 -chrM 833 C 4 .,., IIII 0 0 0 0 4 -chrM 834 G 4 .,., IIII 0 0 0 0 4 -chrM 835 A 4 .,., IIII 0 0 0 0 4 -chrM 836 A 4 .,., 8III 0 0 0 0 4 -chrM 837 A 4 .,., IIII 0 0 0 0 4 -chrM 838 G 4 .,., IIII 0 0 0 0 4 -chrM 839 T 5 .,.,^:, 4:IIG 0 0 0 0 4 -chrM 840 C 5 .,.,, IIIII 0 0 0 0 5 -chrM 841 T 5 .$,.,, IIIII 0 0 0 0 5 -chrM 842 C 4 ,.,, IIII 0 0 0 0 4 -chrM 843 C 4 ,.,, IIII 0 0 0 0 4 -chrM 844 A 4 ,.,, IIII 0 0 0 0 4 -chrM 845 T 4 ,$.,, IIII 0 0 0 0 4 -chrM 846 G 3 .,, @II 0 0 0 0 3 -chrM 847 A 3 .,, III 0 0 0 0 3 -chrM 848 A 3 .,, III 0 0 0 0 3 -chrM 849 A 3 .,, III 0 0 0 0 3 -chrM 850 C 3 .,, III 0 0 0 0 3 -chrM 851 T 3 .,, III 0 0 0 0 3 -chrM 852 G 3 .,, III 0 0 0 0 3 -chrM 853 G 3 .,, III 0 0 0 0 3 -chrM 854 A 3 .,, EII 0 0 0 0 3 -chrM 855 G 3 .,, DII 0 0 0 0 3 -chrM 856 A 3 .,, III 0 0 0 0 3 -chrM 857 C 3 .,, III 0 0 0 0 3 -chrM 858 T 4 .,,^:, IIIA 0 0 0 0 4 -chrM 859 A 4 .,,, @III 0 0 0 0 4 -chrM 860 A 4 .,,, IIII 0 0 0 0 4 -chrM 861 A 4 .$,,, EIII 0 0 0 0 4 -chrM 862 G 3 ,,, III 0 0 0 0 3 -chrM 863 G 3 ,,, III 0 0 0 0 3 -chrM 864 A 3 ,$,, III 0 0 0 0 3 -chrM 905 C 3 ,.^:, III 0 0 0 0 3 -chrM 906 A 3 ,., III 0 0 0 0 3 -chrM 907 G 3 ,., III 0 0 0 0 3 -chrM 908 G 3 ,., III 0 0 0 0 3 -chrM 909 C 3 ,., III 0 0 0 0 3 -chrM 910 C 3 ,., III 0 0 0 0 3 -chrM 911 A 4 ,.,^:, IIII 0 0 0 0 4 -chrM 912 T 4 ,.,, IIEG 0 0 0 0 4 -chrM 913 G 4 ,.,, III: 0 0 0 0 4 -chrM 914 A 4 ,.,, IIII 0 0 0 0 4 -chrM 915 A 4 ,.,, IIII 0 0 0 0 4 -chrM 916 G 4 ,.,, III5 0 0 0 0 4 -chrM 917 C 4 ,.,, III5 0 0 0 0 4 -chrM 918 G 4 ,.,, IIII 0 0 0 0 4 -chrM 919 C 4 ,.,, III< 0 0 0 0 4 -chrM 920 G 4 ,.,, IIII 0 0 0 0 4 -chrM 921 C 4 ,.,, IIII 0 0 0 0 4 -chrM 922 A 4 ,.,, IIII 0 0 0 0 4 -chrM 923 C 4 ,.,, III8 0 0 0 0 4 -chrM 924 A 4 ,.,, IFII 0 0 0 0 4 -chrM 925 C 4 ,.,, IIII 0 0 0 0 4 -chrM 926 A 4 ,.,, IIII 0 0 0 0 4 -chrM 927 C 4 ,.,, IIII 0 0 0 0 4 -chrM 928 C 5 ,.,,^:, IIII: 0 0 0 0 5 -chrM 929 G 5 ,.,,, IIIE: 0 0 0 0 5 -chrM 930 C 5 ,.,,, IIIII 0 0 0 0 5 -chrM 931 C 5 ,.,,, IIIIF 0 0 0 0 5 -chrM 932 C 5 ,.,,, IIIIC 0 0 0 0 5 -chrM 933 G 5 ,$.,,, I?II: 0 0 0 0 5 -chrM 934 T 4 .$,,, 4II> 0 0 0 0 3 -chrM 935 C 3 ,,, III 0 0 0 0 3 -chrM 936 A 3 ,,, III 0 0 0 0 3 -chrM 937 C 3 ,,, II1 0 0 0 0 2 -chrM 938 C 3 ,,, III 0 0 0 0 3 -chrM 939 C 3 ,,, III 0 0 0 0 3 -chrM 940 T 3 ,$,, III 0 0 0 0 3 -chrM 958 C 3 ,.^:. III 0 0 0 0 3 -chrM 959 A 3 ,.. III 0 0 0 0 3 -chrM 960 T 3 ,.. III 0 0 0 0 3 -chrM 961 A 3 ,.. III 0 0 0 0 3 -chrM 962 A 3 ,.. III 0 0 0 0 3 -chrM 963 C 4 ,$..^:. IIII 0 0 0 0 4 -chrM 964 A 3 ... I(; 0 0 0 0 2 -chrM 965 T 3 ... III 0 0 0 0 3 -chrM 966 A 4 ...^:. IIII 0 0 0 0 4 -chrM 967 A 4 .... IIII 0 0 0 0 4 -chrM 968 C 4 .... IEII 0 0 0 0 4 -chrM 969 A 4 .... IIII 0 0 0 0 4 -chrM 970 T 4 .... IIII 0 0 0 0 4 -chrM 971 A 4 .... IIII 0 0 0 0 4 -chrM 972 A 4 .... IIII 0 0 0 0 4 -chrM 973 A 4 .... II0I 0 0 0 0 3 -chrM 974 A 5 ....^:. IIIII 0 0 0 0 5 -chrM 975 C 5 ..... IIIII 0 0 0 0 5 -chrM 976 C 5 ..... IIIII 0 0 0 0 5 -chrM 977 G 5 ..... IIIII 0 0 0 0 5 -chrM 978 T 5 ..... IIIII 0 0 0 0 5 -chrM 979 G 5 ..... I0III 0 0 0 0 4 -chrM 980 A 5 ..... IIII4 0 0 0 0 4 -chrM 981 C 5 ..... IIIII 0 0 0 0 5 -chrM 982 C 5 ..... IIIII 0 0 0 0 5 -chrM 983 C 5 ..... IIIII 0 0 0 0 5 -chrM 984 A 5 ..... -IGII 0 0 0 0 4 -chrM 985 A 5 ..... 4GIII 0 0 0 0 4 -chrM 986 A 5 ..... BDGII 0 0 0 0 5 -chrM 987 C 5 ..... IDIII 0 0 0 0 5 -chrM 988 A 5 ..... @<III 0 0 0 0 5 -chrM 989 T 5 ..... IIIII 0 0 0 0 5 -chrM 990 A 5 .$.... I@III 0 0 0 0 5 -chrM 991 T 4 .... IICI 0 0 0 0 4 -chrM 992 G 4 T... )III 0 0 0 0 3 -chrM 993 A 4 .$... ?ICI 0 0 0 0 4 -chrM 994 A 3 ... III 0 0 0 0 3 -chrM 995 A 3 ... III 0 0 0 0 3 -chrM 996 G 3 ... III 0 0 0 0 3 -chrM 997 G 3 ... III 0 0 0 0 3 -chrM 998 A 3 .$.. 4II 0 0 0 0 2 -chrM 999 G 3 ..^:. III 0 0 0 0 3 -chrM 1000 A 3 ... III 0 0 0 0 3 -chrM 1001 C 3 .$.. III 0 0 0 0 3 -chrM 1043 A 3 ..^:, III 0 0 0 0 3 -chrM 1044 A 3 .., III 0 0 0 0 3 -chrM 1045 C 3 .., II7 0 0 0 0 3 -chrM 1046 C 3 .., II- 0 0 0 0 2 -chrM 1047 A 3 .., III 0 0 0 0 3 -chrM 1048 A 3 .., III 0 0 0 0 3 -chrM 1049 A 3 .., III 0 0 0 0 3 -chrM 1050 G 3 .., III 0 0 0 0 3 -chrM 1051 T 3 .., III 0 0 0 0 3 -chrM 1052 G 3 .., III 0 0 0 0 3 -chrM 1053 T 3 .., GII 0 0 0 0 3 -chrM 1054 A 3 .., III 0 0 0 0 3 -chrM 1055 G 3 .., :II 0 0 0 0 3 -chrM 1056 C 3 ..a HI% 0 0 0 0 2 -chrM 1057 T 3 .., III 0 0 0 0 3 -chrM 1058 T 3 .., III 0 0 0 0 3 -chrM 1059 A 3 .., BII 0 0 0 0 3 -chrM 1060 A 3 .., GII 0 0 0 0 3 -chrM 1061 A 3 .., HII 0 0 0 0 3 -chrM 1062 C 3 .., III 0 0 0 0 3 -chrM 1063 A 3 .., DII 0 0 0 0 3 -chrM 1064 A 3 .., BII 0 0 0 0 3 -chrM 1065 A 3 .., 1II 0 0 0 0 2 -chrM 1066 G 3 .$., &II 0 0 0 0 2 +chrM 416 G 5 ...,^:, II?7: 0 0 5 0 5 +chrM 417 T 5 ...,, ;IIE@ 0 0 0 5 5 +chrM 418 A 5 ...,, IIIII 5 0 0 0 5 +chrM 419 A 5 ...,, IIIII 5 0 0 0 5 +chrM 420 A 5 ...,, FIIII 5 0 0 0 5 +chrM 421 A 5 ...,, IIIII 5 0 0 0 5 +chrM 422 A 5 ...,, >IIII 5 0 0 0 5 +chrM 423 G 6 ...,,^:, HII/I, 0 0 4 0 4 +chrM 424 C 6 .$..a,, ;II-I: 0 5 0 0 5 +chrM 425 T 5 .$.,,, IIIIF 0 0 0 5 5 +chrM 426 A 5 .,,,^:, III@I 5 0 0 0 5 +chrM 427 C 5 .,,,, III$I 0 4 0 0 4 +chrM 428 A 5 .,,,, IIIII 5 0 0 0 5 +chrM 429 A 5 .,,,, IIII. 4 0 0 0 4 +chrM 430 C 5 .,,,a I%I5' 0 3 0 0 3 +chrM 431 C 5 .,,,, I(I5< 0 4 0 0 4 +chrM 432 A 5 .,,,, IIIII 5 0 0 0 5 +chrM 433 A 5 .,,,, 0IIII 4 0 0 0 4 +chrM 434 A 5 .,,,, =IIII 5 0 0 0 5 +chrM 435 G 5 .$,,,, EIIII 0 0 5 0 5 +chrM 436 T 4 ,,,, III5 0 0 0 4 4 +chrM 437 A 4 ,,,, IIII 4 0 0 0 4 +chrM 438 A 4 ,,,, IIII 4 0 0 0 4 +chrM 439 A 4 ,,,, IIII 4 0 0 0 4 +chrM 440 A 4 ,,,, IIIF 4 0 0 0 4 +chrM 441 T 6 ,,,,^:.^:. III;II 0 0 0 6 6 +chrM 442 A 6 ,,,,.. IIIIII 6 0 0 0 6 +chrM 443 G 6 ,,,,.. IIIIII 0 0 6 0 6 +chrM 444 A 6 ,,,,.. IIIIII 6 0 0 0 6 +chrM 445 C 6 ,,,,.. IIIIII 0 6 0 0 6 +chrM 446 T 6 ,$,,,.. IIIIII 0 0 0 6 6 +chrM 447 A 5 ,,,.. IIIII 5 0 0 0 5 +chrM 448 C 5 ,,,.. IIIII 0 5 0 0 5 +chrM 449 G 6 ,,,..^:, IIIII6 0 0 6 0 6 +chrM 450 A 6 ,,,.., IIIIII 6 0 0 0 6 +chrM 451 A 6 ,$,,.., IIIIII 6 0 0 0 6 +chrM 452 A 5 ,,.., IIIII 5 0 0 0 5 +chrM 453 G 5 ,,.., IIIII 0 0 5 0 5 +chrM 454 T 6 ,,..,^:, IIIIII 0 0 0 6 6 +chrM 455 G 6 ,,..,, IIIIII 0 0 6 0 6 +chrM 456 A 6 ,,..,, IIIIII 6 0 0 0 6 +chrM 457 C 6 ,,..,, IIIII= 0 6 0 0 6 +chrM 458 T 6 ,$,..,, IIIIII 0 0 0 6 6 +chrM 459 T 5 ,..,, IIIII 0 0 0 5 5 +chrM 460 T 5 ,..,, IIIII 0 0 0 5 5 +chrM 461 A 5 ,$..,, IIIII 5 0 0 0 5 +chrM 462 A 4 ..,, IIII 4 0 0 0 4 +chrM 463 T 4 ..,, IIIC 0 0 0 4 4 +chrM 464 A 4 ..,, IIII 4 0 0 0 4 +chrM 465 C 4 ..,, IIII 0 4 0 0 4 +chrM 466 C 4 ..,, IIII 0 4 0 0 4 +chrM 467 T 4 ..,, II>? 0 0 0 4 4 +chrM 468 C 4 ..,, IIII 0 4 0 0 4 +chrM 469 T 4 ..,, IIIG 0 0 0 4 4 +chrM 470 G 4 ..,, %III 0 0 3 0 3 +chrM 471 A 4 ..,, 4;II 3 0 0 0 3 +chrM 472 C 4 ..,, II3I 0 3 0 0 3 +chrM 473 T 4 ..,, IIII 0 0 0 4 4 +chrM 474 A 4 ..,, ;III 4 0 0 0 4 +chrM 475 C 4 ..,, IIII 0 4 0 0 4 +chrM 476 A 4 .$.$,, 32II 2 0 0 0 2 +chrM 480 T 3 ,,^:. III 0 0 0 3 3 +chrM 481 A 3 ,,. III 3 0 0 0 3 +chrM 482 G 3 ,,. III 0 0 3 0 3 +chrM 483 C 4 ,,.^:, IIIE 0 4 0 0 4 +chrM 484 T 4 ,$,., III9 0 0 0 4 4 +chrM 485 A 3 ,., III 3 0 0 0 3 +chrM 486 A 3 ,., III 3 0 0 0 3 +chrM 487 G 3 ,., III 0 0 3 0 3 +chrM 488 A 3 ,., III 3 0 0 0 3 +chrM 489 C 3 ,$., III 0 3 0 0 3 +chrM 510 C 3 .,^:. III 0 3 0 0 3 +chrM 511 C 3 .,. III 0 3 0 0 3 +chrM 512 A 3 .,. 6II 3 0 0 0 3 +chrM 513 C 3 .,. III 0 3 0 0 3 +chrM 514 T 3 .,. III 0 0 0 3 3 +chrM 515 A 3 .$,. III 3 0 0 0 3 +chrM 518 C 3 ,$.^:. III 0 3 0 0 3 +chrM 520 T 3 ..^:, III 0 0 0 3 3 +chrM 521 A 3 .., III 3 0 0 0 3 +chrM 522 G 3 .., II, 0 0 2 0 2 +chrM 523 C 3 .., III 0 3 0 0 3 +chrM 524 C 3 .., II7 0 3 0 0 3 +chrM 525 C 3 .., III 0 3 0 0 3 +chrM 526 T 3 .., II? 0 0 0 3 3 +chrM 527 A 3 .., III 3 0 0 0 3 +chrM 528 A 3 .., III 3 0 0 0 3 +chrM 529 A 3 .., FII 3 0 0 0 3 +chrM 530 C 3 .., II+ 0 2 0 0 2 +chrM 531 T 3 .., III 0 0 0 3 3 +chrM 532 A 3 .., :II 3 0 0 0 3 +chrM 533 A 3 .., DGI 3 0 0 0 3 +chrM 534 A 3 .., III 3 0 0 0 3 +chrM 535 A 3 .., ?CI 3 0 0 0 3 +chrM 536 T 3 .., III 0 0 0 3 3 +chrM 537 A 3 .., 9II 3 0 0 0 3 +chrM 538 G 3 .., III 0 0 3 0 3 +chrM 539 C 3 .., III 0 3 0 0 3 +chrM 540 T 3 .., III 0 0 0 3 3 +chrM 541 T 3 .., III 0 0 0 3 3 +chrM 542 A 4 ..,^:. IIII 4 0 0 0 4 +chrM 543 C 4 ..,. IIII 0 4 0 0 4 +chrM 544 C 4 ..,. IIII 0 4 0 0 4 +chrM 545 A 4 N$.,. "III 3 0 0 0 3 +chrM 546 C 3 .,. III 0 3 0 0 3 +chrM 547 A 3 .,. DII 3 0 0 0 3 +chrM 548 A 3 .,. EII 3 0 0 0 3 +chrM 549 C 3 .,. III 0 3 0 0 3 +chrM 550 A 3 .,. III 3 0 0 0 3 +chrM 551 A 3 .,. 6II 3 0 0 0 3 +chrM 552 A 3 .,. GII 3 0 0 0 3 +chrM 553 G 3 .$,. ?II 0 0 3 0 3 +chrM 577 A 3 .$.^:. III 3 0 0 0 3 +chrM 580 A 3 ..^:, III 3 0 0 0 3 +chrM 581 G 3 .., III 0 0 3 0 3 +chrM 582 C 3 .., II? 0 3 0 0 3 +chrM 583 C 3 ..a II- 0 2 0 0 2 +chrM 584 T 3 .., IIH 0 0 0 3 3 +chrM 585 A 3 .., III 3 0 0 0 3 +chrM 586 A 3 .., III 3 0 0 0 3 +chrM 587 A 4 ..,^:, IIII 4 0 0 0 4 +chrM 588 A 4 ..,, IIII 4 0 0 0 4 +chrM 589 C 4 ..,, IIII 0 4 0 0 4 +chrM 590 T 4 ..,, II.5 0 0 0 3 3 +chrM 591 C 4 .$.,, II<I 0 4 0 0 4 +chrM 592 A 3 .,, III 3 0 0 0 3 +chrM 593 A 3 .,, III 3 0 0 0 3 +chrM 594 A 3 .,, III 3 0 0 0 3 +chrM 595 G 3 .,, III 0 0 3 0 3 +chrM 596 G 3 .,, III 0 0 3 0 3 +chrM 597 A 3 .,, :EI 3 0 0 0 3 +chrM 598 C 3 .,, III 0 3 0 0 3 +chrM 599 T 4 .,,^:. II@I 0 0 0 4 4 +chrM 600 T 4 .,,. IIII 0 0 0 4 4 +chrM 601 G 4 .,,. IIII 0 0 4 0 4 +chrM 602 G 4 .,,. IIII 0 0 4 0 4 +chrM 603 C 4 .,,. IIII 0 4 0 0 4 +chrM 604 G 4 .,,. IIII 0 0 4 0 4 +chrM 605 G 4 .,,. IIII 0 0 4 0 4 +chrM 606 T 4 .,,. 5III 0 0 0 4 4 +chrM 607 G 4 .,,. IIII 0 0 4 0 4 +chrM 608 C 4 .,,. *III 0 3 0 0 3 +chrM 609 T 5 .,,.^:, ?IIII 0 0 0 5 5 +chrM 610 T 5 .,,., IIII8 0 0 0 5 5 +chrM 611 T 5 .,,., IIIII 0 0 0 5 5 +chrM 612 A 5 T$,,., 3IIII 4 0 0 0 4 +chrM 613 C 4 ,,., III) 0 3 0 0 3 +chrM 614 A 4 ,,., IIII 4 0 0 0 4 +chrM 615 T 4 ,$,., IIII 0 0 0 4 4 +chrM 616 C 3 ,., III 0 3 0 0 3 +chrM 617 C 3 ,., III 0 3 0 0 3 +chrM 618 C 3 ,., III 0 3 0 0 3 +chrM 619 T 3 ,., IF9 0 0 0 3 3 +chrM 620 C 3 ,., II7 0 3 0 0 3 +chrM 621 T 3 ,., III 0 0 0 3 3 +chrM 622 A 3 ,$., I7I 3 0 0 0 3 +chrM 652 C 3 .,^:, II) 0 2 0 0 2 +chrM 653 G 3 .,, II2 0 0 2 0 2 +chrM 654 A 3 .,, III 3 0 0 0 3 +chrM 655 T 4 .,,^:. II*I 0 0 0 3 3 +chrM 656 A 4 .,,. IIII 4 0 0 0 4 +chrM 657 A 4 .,,. IIII 4 0 0 0 4 +chrM 658 A 4 .,,. IIII 4 0 0 0 4 +chrM 659 C 4 .,,. IIII 0 4 0 0 4 +chrM 660 C 4 .,,. IIII 0 4 0 0 4 +chrM 661 C 4 .,,. IIII 0 4 0 0 4 +chrM 662 C 4 .,,. IIFI 0 4 0 0 4 +chrM 663 A 4 .,,. =IDI 4 0 0 0 4 +chrM 664 C 4 .,,. II6I 0 4 0 0 4 +chrM 665 C 5 .,,.^:, IIIII 0 5 0 0 5 +chrM 666 A 5 .,,., BIIII 5 0 0 0 5 +chrM 667 T 5 .,,., II5I+ 0 0 0 4 4 +chrM 668 C 5 .,,., IIIII 0 5 0 0 5 +chrM 669 C 5 .,,., IIIII 0 5 0 0 5 +chrM 670 C 5 .,a., II.II 0 4 0 0 4 +chrM 671 T 5 .,,., IIIIA 0 0 0 5 5 +chrM 672 T 6 .,,.,^:. FI9I.I 0 0 0 5 5 +chrM 673 G 6 .,,.,. IIIIII 0 0 6 0 6 +chrM 674 C 6 .,,.,. IIIIII 0 6 0 0 6 +chrM 675 T 6 .,,.,. IIIIII 0 0 0 6 6 +chrM 676 A 6 .,,.,. ,IIEII 5 0 0 0 5 +chrM 677 A 7 .,,.,.^:. 3II;III 6 0 0 0 6 +chrM 678 T 7 .,,.,.. IIIIDII 0 0 0 7 7 +chrM 679 T 7 .,,.,.. CIIIIII 0 0 0 7 7 +chrM 680 C 7 .,,.,.. IIIIIII 0 7 0 0 7 +chrM 681 A 7 .$,,.,.. 9IIIIII 7 0 0 0 7 +chrM 682 G 6 ,,.,.. II$III 0 0 5 0 5 +chrM 683 C 6 ,,.,.. IIIIII 0 6 0 0 6 +chrM 684 C 6 ,$,.,.. IIIIII 0 6 0 0 6 +chrM 685 T 5 ,.,.. IIIII 0 0 0 5 5 +chrM 686 A 5 ,.,.. IIIII 5 0 0 0 5 +chrM 687 T 5 ,$.,.. IIIII 0 0 0 5 5 +chrM 688 A 4 .,.. IIII 4 0 0 0 4 +chrM 689 T 4 .,.. IIII 0 0 0 4 4 +chrM 690 A 4 .$,.. IIII 4 0 0 0 4 +chrM 691 C 3 ,.. III 0 3 0 0 3 +chrM 692 C 3 ,.. III 0 3 0 0 3 +chrM 693 G 4 ,..^:, IIII 0 0 4 0 4 +chrM 694 C 4 ,.., IIII 0 4 0 0 4 +chrM 695 C 4 ,.., IIII 0 4 0 0 4 +chrM 696 A 4 ,.., IIII 4 0 0 0 4 +chrM 697 T 4 ,.., IIII 0 0 0 4 4 +chrM 698 C 4 ,.., IIII 0 4 0 0 4 +chrM 699 T 4 ,.., IIII 0 0 0 4 4 +chrM 700 T 4 ,$.., IIII 0 0 0 4 4 +chrM 701 C 3 .., III 0 3 0 0 3 +chrM 702 A 3 .., III 3 0 0 0 3 +chrM 703 G 3 .., 2II 0 0 2 0 2 +chrM 704 C 3 .., III 0 3 0 0 3 +chrM 705 A 3 N., "II 2 0 0 0 2 +chrM 706 A 3 .., I5I 3 0 0 0 3 +chrM 707 A 3 .$., GII 3 0 0 0 3 +chrM 726 A 3 ,,^:. III 3 0 0 0 3 +chrM 727 G 3 ,,. III 0 0 3 0 3 +chrM 728 T 3 ,$,. III 0 0 0 3 3 +chrM 732 C 3 a.^:. $II 0 2 0 0 2 +chrM 733 A 3 ,.. III 3 0 0 0 3 +chrM 734 C 3 ,.. %II 0 2 0 0 2 +chrM 735 A 3 ,.. III 3 0 0 0 3 +chrM 736 A 3 ,.. *II 2 0 0 0 2 +chrM 737 A 3 ,.. III 3 0 0 0 3 +chrM 738 T 3 ,.. III 0 0 0 3 3 +chrM 739 A 3 ,.. III 3 0 0 0 3 +chrM 740 T 3 ,.. III 0 0 0 3 3 +chrM 741 C 3 ,.. III 0 3 0 0 3 +chrM 742 C 3 ,.. III 0 3 0 0 3 +chrM 743 A 3 ,.. III 3 0 0 0 3 +chrM 744 A 3 ,.. III 3 0 0 0 3 +chrM 745 C 3 ,.. III 0 3 0 0 3 +chrM 746 A 3 ,.. IIE 3 0 0 0 3 +chrM 747 T 3 ,.. III 0 0 0 3 3 +chrM 748 A 3 ,.. III 3 0 0 0 3 +chrM 749 A 3 ,.. III 3 0 0 0 3 +chrM 750 A 3 ,.. III 3 0 0 0 3 +chrM 751 A 3 ,.. IAI 3 0 0 0 3 +chrM 752 A 3 ,.. III 3 0 0 0 3 +chrM 753 C 3 ,.. III 0 3 0 0 3 +chrM 754 G 3 ,$.. III 0 0 3 0 3 +chrM 756 T 3 ..^:, III 0 0 0 3 3 +chrM 757 A 3 .., III 3 0 0 0 3 +chrM 758 G 3 .., III 0 0 3 0 3 +chrM 759 G 3 .., III 0 0 3 0 3 +chrM 760 T 3 .., =II 0 0 0 3 3 +chrM 761 C 3 .$., IID 0 3 0 0 3 +chrM 767 G 3 .$,^:, III 0 0 3 0 3 +chrM 769 A 3 ,,^:, III 3 0 0 0 3 +chrM 770 G 3 ,,, III 0 0 3 0 3 +chrM 771 C 3 ,,, IHI 0 3 0 0 3 +chrM 772 C 3 ,a, I)/ 0 1 0 0 1 +chrM 773 C 3 ,,, I7I 0 3 0 0 3 +chrM 774 A 4 ,,,^:. II:I 4 0 0 0 4 +chrM 775 T 4 ,,,. IH.I 0 0 0 3 3 +chrM 776 G 4 ,,,. IIII 0 0 4 0 4 +chrM 777 G 4 ,,,. IIII 0 0 4 0 4 +chrM 778 G 4 ,,,. IIII 0 0 4 0 4 +chrM 779 A 4 ,,,. IIAI 4 0 0 0 4 +chrM 780 T 4 ,,,. IIGI 0 0 0 4 4 +chrM 781 G 4 ,,,. IIII 0 0 4 0 4 +chrM 782 G 4 ,,,. IIII 0 0 4 0 4 +chrM 783 A 4 ,,,. IIII 4 0 0 0 4 +chrM 784 G 4 ,,,. IIII 0 0 4 0 4 +chrM 785 A 4 ,,,. IIII 4 0 0 0 4 +chrM 786 G 4 ,,,. IIII 0 0 4 0 4 +chrM 787 A 4 ,,,. IIII 4 0 0 0 4 +chrM 788 A 4 ,,,. IIII 4 0 0 0 4 +chrM 789 A 4 ,,,. IIII 4 0 0 0 4 +chrM 790 T 5 ,,,.^:. IIIII 0 0 0 5 5 +chrM 791 G 5 ,$,,.. IIIII 0 0 5 0 5 +chrM 792 G 4 ,,.. IIII 0 0 4 0 4 +chrM 793 G 4 ,,.. IIII 0 0 4 0 4 +chrM 794 C 4 ,,.. IIII 0 4 0 0 4 +chrM 795 T 4 ,,.. IIII 0 0 0 4 4 +chrM 796 A 4 ,,.. IIII 4 0 0 0 4 +chrM 797 C 4 ,,.. IIII 0 4 0 0 4 +chrM 798 A 4 ,,.. IIII 4 0 0 0 4 +chrM 799 T 4 ,,.. IIII 0 0 0 4 4 +chrM 800 T 4 ,,.. IIII 0 0 0 4 4 +chrM 801 T 4 ,,.. IIII 0 0 0 4 4 +chrM 802 T 4 ,$,.. IIII 0 0 0 4 4 +chrM 803 C 3 ,.. III 0 3 0 0 3 +chrM 804 T 3 ,$.. III 0 0 0 3 3 +chrM 806 C 3 ..^:. III 0 3 0 0 3 +chrM 807 C 3 ... III 0 3 0 0 3 +chrM 808 C 3 ... III 0 3 0 0 3 +chrM 809 T 3 .$.. III 0 0 0 3 3 +chrM 810 A 3 ..^:, III 3 0 0 0 3 +chrM 811 A 3 .., III 3 0 0 0 3 +chrM 812 G 3 .., II7 0 0 3 0 3 +chrM 813 A 3 .., III 3 0 0 0 3 +chrM 814 A 3 .., III 3 0 0 0 3 +chrM 815 C 3 .., III 0 3 0 0 3 +chrM 816 A 3 .., III 3 0 0 0 3 +chrM 817 A 3 .., III 3 0 0 0 3 +chrM 818 G 3 .., III 0 0 3 0 3 +chrM 819 A 3 .., III 3 0 0 0 3 +chrM 820 A 3 .., &II 2 0 0 0 2 +chrM 821 C 3 .., III 0 3 0 0 3 +chrM 822 T 3 .., III 0 0 0 3 3 +chrM 823 T 3 ..n II" 0 0 0 2 2 +chrM 824 T 3 .., III 0 0 0 3 3 +chrM 825 A 3 .$., III 3 0 0 0 3 +chrM 826 A 3 .,^:. III 3 0 0 0 3 +chrM 827 C 3 .,. III 0 3 0 0 3 +chrM 828 C 3 .,. III 0 3 0 0 3 +chrM 829 C 4 .,.^:, IIII 0 4 0 0 4 +chrM 830 G 4 .,., IIII 0 0 4 0 4 +chrM 831 G 4 .,., IIII 0 0 4 0 4 +chrM 832 A 4 .,., IIII 4 0 0 0 4 +chrM 833 C 4 .,., IIII 0 4 0 0 4 +chrM 834 G 4 .,., IIII 0 0 4 0 4 +chrM 835 A 4 .,., IIII 4 0 0 0 4 +chrM 836 A 4 .,., 8III 4 0 0 0 4 +chrM 837 A 4 .,., IIII 4 0 0 0 4 +chrM 838 G 4 .,., IIII 0 0 4 0 4 +chrM 839 T 5 .,.,^:, 4:IIG 0 0 0 4 4 +chrM 840 C 5 .,.,, IIIII 0 5 0 0 5 +chrM 841 T 5 .$,.,, IIIII 0 0 0 5 5 +chrM 842 C 4 ,.,, IIII 0 4 0 0 4 +chrM 843 C 4 ,.,, IIII 0 4 0 0 4 +chrM 844 A 4 ,.,, IIII 4 0 0 0 4 +chrM 845 T 4 ,$.,, IIII 0 0 0 4 4 +chrM 846 G 3 .,, @II 0 0 3 0 3 +chrM 847 A 3 .,, III 3 0 0 0 3 +chrM 848 A 3 .,, III 3 0 0 0 3 +chrM 849 A 3 .,, III 3 0 0 0 3 +chrM 850 C 3 .,, III 0 3 0 0 3 +chrM 851 T 3 .,, III 0 0 0 3 3 +chrM 852 G 3 .,, III 0 0 3 0 3 +chrM 853 G 3 .,, III 0 0 3 0 3 +chrM 854 A 3 .,, EII 3 0 0 0 3 +chrM 855 G 3 .,, DII 0 0 3 0 3 +chrM 856 A 3 .,, III 3 0 0 0 3 +chrM 857 C 3 .,, III 0 3 0 0 3 +chrM 858 T 4 .,,^:, IIIA 0 0 0 4 4 +chrM 859 A 4 .,,, @III 4 0 0 0 4 +chrM 860 A 4 .,,, IIII 4 0 0 0 4 +chrM 861 A 4 .$,,, EIII 4 0 0 0 4 +chrM 862 G 3 ,,, III 0 0 3 0 3 +chrM 863 G 3 ,,, III 0 0 3 0 3 +chrM 864 A 3 ,$,, III 3 0 0 0 3 +chrM 905 C 3 ,.^:, III 0 3 0 0 3 +chrM 906 A 3 ,., III 3 0 0 0 3 +chrM 907 G 3 ,., III 0 0 3 0 3 +chrM 908 G 3 ,., III 0 0 3 0 3 +chrM 909 C 3 ,., III 0 3 0 0 3 +chrM 910 C 3 ,., III 0 3 0 0 3 +chrM 911 A 4 ,.,^:, IIII 4 0 0 0 4 +chrM 912 T 4 ,.,, IIEG 0 0 0 4 4 +chrM 913 G 4 ,.,, III: 0 0 4 0 4 +chrM 914 A 4 ,.,, IIII 4 0 0 0 4 +chrM 915 A 4 ,.,, IIII 4 0 0 0 4 +chrM 916 G 4 ,.,, III5 0 0 4 0 4 +chrM 917 C 4 ,.,, III5 0 4 0 0 4 +chrM 918 G 4 ,.,, IIII 0 0 4 0 4 +chrM 919 C 4 ,.,, III< 0 4 0 0 4 +chrM 920 G 4 ,.,, IIII 0 0 4 0 4 +chrM 921 C 4 ,.,, IIII 0 4 0 0 4 +chrM 922 A 4 ,.,, IIII 4 0 0 0 4 +chrM 923 C 4 ,.,, III8 0 4 0 0 4 +chrM 924 A 4 ,.,, IFII 4 0 0 0 4 +chrM 925 C 4 ,.,, IIII 0 4 0 0 4 +chrM 926 A 4 ,.,, IIII 4 0 0 0 4 +chrM 927 C 4 ,.,, IIII 0 4 0 0 4 +chrM 928 C 5 ,.,,^:, IIII: 0 5 0 0 5 +chrM 929 G 5 ,.,,, IIIE: 0 0 5 0 5 +chrM 930 C 5 ,.,,, IIIII 0 5 0 0 5 +chrM 931 C 5 ,.,,, IIIIF 0 5 0 0 5 +chrM 932 C 5 ,.,,, IIIIC 0 5 0 0 5 +chrM 933 G 5 ,$.,,, I?II: 0 0 5 0 5 +chrM 934 T 4 .$,,, 4II> 0 0 0 3 3 +chrM 935 C 3 ,,, III 0 3 0 0 3 +chrM 936 A 3 ,,, III 3 0 0 0 3 +chrM 937 C 3 ,,, II1 0 2 0 0 2 +chrM 938 C 3 ,,, III 0 3 0 0 3 +chrM 939 C 3 ,,, III 0 3 0 0 3 +chrM 940 T 3 ,$,, III 0 0 0 3 3 +chrM 958 C 3 ,.^:. III 0 3 0 0 3 +chrM 959 A 3 ,.. III 3 0 0 0 3 +chrM 960 T 3 ,.. III 0 0 0 3 3 +chrM 961 A 3 ,.. III 3 0 0 0 3 +chrM 962 A 3 ,.. III 3 0 0 0 3 +chrM 963 C 4 ,$..^:. IIII 0 4 0 0 4 +chrM 964 A 3 ... I(; 2 0 0 0 2 +chrM 965 T 3 ... III 0 0 0 3 3 +chrM 966 A 4 ...^:. IIII 4 0 0 0 4 +chrM 967 A 4 .... IIII 4 0 0 0 4 +chrM 968 C 4 .... IEII 0 4 0 0 4 +chrM 969 A 4 .... IIII 4 0 0 0 4 +chrM 970 T 4 .... IIII 0 0 0 4 4 +chrM 971 A 4 .... IIII 4 0 0 0 4 +chrM 972 A 4 .... IIII 4 0 0 0 4 +chrM 973 A 4 .... II0I 3 0 0 0 3 +chrM 974 A 5 ....^:. IIIII 5 0 0 0 5 +chrM 975 C 5 ..... IIIII 0 5 0 0 5 +chrM 976 C 5 ..... IIIII 0 5 0 0 5 +chrM 977 G 5 ..... IIIII 0 0 5 0 5 +chrM 978 T 5 ..... IIIII 0 0 0 5 5 +chrM 979 G 5 ..... I0III 0 0 4 0 4 +chrM 980 A 5 ..... IIII4 4 0 0 0 4 +chrM 981 C 5 ..... IIIII 0 5 0 0 5 +chrM 982 C 5 ..... IIIII 0 5 0 0 5 +chrM 983 C 5 ..... IIIII 0 5 0 0 5 +chrM 984 A 5 ..... -IGII 4 0 0 0 4 +chrM 985 A 5 ..... 4GIII 4 0 0 0 4 +chrM 986 A 5 ..... BDGII 5 0 0 0 5 +chrM 987 C 5 ..... IDIII 0 5 0 0 5 +chrM 988 A 5 ..... @<III 5 0 0 0 5 +chrM 989 T 5 ..... IIIII 0 0 0 5 5 +chrM 990 A 5 .$.... I@III 5 0 0 0 5 +chrM 991 T 4 .... IICI 0 0 0 4 4 +chrM 992 G 4 T... )III 0 0 3 0 3 +chrM 993 A 4 .$... ?ICI 4 0 0 0 4 +chrM 994 A 3 ... III 3 0 0 0 3 +chrM 995 A 3 ... III 3 0 0 0 3 +chrM 996 G 3 ... III 0 0 3 0 3 +chrM 997 G 3 ... III 0 0 3 0 3 +chrM 998 A 3 .$.. 4II 2 0 0 0 2 +chrM 999 G 3 ..^:. III 0 0 3 0 3 +chrM 1000 A 3 ... III 3 0 0 0 3 +chrM 1001 C 3 .$.. III 0 3 0 0 3 +chrM 1043 A 3 ..^:, III 3 0 0 0 3 +chrM 1044 A 3 .., III 3 0 0 0 3 +chrM 1045 C 3 .., II7 0 3 0 0 3 +chrM 1046 C 3 .., II- 0 2 0 0 2 +chrM 1047 A 3 .., III 3 0 0 0 3 +chrM 1048 A 3 .., III 3 0 0 0 3 +chrM 1049 A 3 .., III 3 0 0 0 3 +chrM 1050 G 3 .., III 0 0 3 0 3 +chrM 1051 T 3 .., III 0 0 0 3 3 +chrM 1052 G 3 .., III 0 0 3 0 3 +chrM 1053 T 3 .., GII 0 0 0 3 3 +chrM 1054 A 3 .., III 3 0 0 0 3 +chrM 1055 G 3 .., :II 0 0 3 0 3 +chrM 1056 C 3 ..a HI% 0 2 0 0 2 +chrM 1057 T 3 .., III 0 0 0 3 3 +chrM 1058 T 3 .., III 0 0 0 3 3 +chrM 1059 A 3 .., BII 3 0 0 0 3 +chrM 1060 A 3 .., GII 3 0 0 0 3 +chrM 1061 A 3 .., HII 3 0 0 0 3 +chrM 1062 C 3 .., III 0 3 0 0 3 +chrM 1063 A 3 .., DII 3 0 0 0 3 +chrM 1064 A 3 .., BII 3 0 0 0 3 +chrM 1065 A 3 .., 1II 2 0 0 0 2 +chrM 1066 G 3 .$., &II 0 0 2 0 2 diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.6col.20-3-yes-no.pileup.out --- a/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,2 +1,2 @@ -chrM 270 C 4 a... ;III 1 0 0 0 4 +chrM 270 C 4 a... ;III 1 3 0 0 4 chrM 415 C 4 TTTt III7 0 0 0 4 4 diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.6col.20-3-yes-yes.pileup.out --- a/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,2 +1,2 @@ -chrM 269 270 C 4 a... ;III 1 0 0 0 4 +chrM 269 270 C 4 a... ;III 1 3 0 0 4 chrM 414 415 C 4 TTTt III7 0 0 0 4 4 diff -r 517bd810a6b2 -r be8f54671d56 tools/samtools/pileup_parser.pl --- a/tools/samtools/pileup_parser.pl Thu Jan 14 11:26:08 2010 -0500 +++ b/tools/samtools/pileup_parser.pl Thu Jan 14 14:07:05 2010 -0500 @@ -65,7 +65,9 @@ { $SNPs_exist = 1; $SNPs{ uc( $bases[ $base ] ) } += 1; - } + } elsif ( $bases[ $base ] =~ m/[.,]/ ) { + $SNPs{ uc( $fields[ $ref_base_column ] ) } += 1; + } } } diff -r 517bd810a6b2 -r be8f54671d56 tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Jan 14 11:26:08 2010 -0500 +++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:07:05 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="pileup_parser" name="Filter pileup"> +<tool id="pileup_parser" name="Filter pileup" version="1.0.1">> <description>on coverage and SNPs</description> <command interpreter="perl"> #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 @@ -189,7 +189,7 @@
you will get::
- chrM 413 G 4 ..t, IIIH 0 0 0 1 3 + chrM 413 G 4 ..t, IIIH 0 0 2 1 3 chrM 415 C 4 TTTt III7 0 0 0 4 4
where:: @@ -211,7 +211,7 @@
and if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column::
- chrM 412 413 G 4 ..t, III2 0 0 0 1 3 + chrM 412 413 G 4 ..t, III2 0 0 2 1 3 chrM 414 415 C 4 TTTt III7 0 0 0 4 4
where::