#@
Paralyzer1.1 Bug:  ConversionPercent >1 (often!) here==4.0:
reczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b$ grep "ENSMUST00000002320,-,949,1195" sh-distributions-0hrep1.txt2
grep: sh-distributions-0hrep1.txt2: No such file or directory
]0;/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1breczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b$ grep "ENSMUST00000002320,-,949,1195" sh-distributions-0hrep1.txt20
ENSMUST00000002320,-,949,1195,G701,Signal,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758275E-5,4.373216008275856E-5,4.3732160082764055E-5,4.37321600828568E-5,4.3732160084257584E-5,4.373216010317043E-5,4.373216033143096E-5,4.373216279365613E-5,4.3732186527830366E-5,4.3732390929367776E-5,4.373396330899324E-5,4.3744764595421976E-5,4.3811001175329695E-5,4.417345831457111E-5,4.5942544706286866E-5,5.3639658099379176E-5,8.34720548677016E-5,1.863797732857121E-4,5.019681953053525E-4,0.001361131453932042,0.0034335167172029907,0.007850752457529421,0.016139127793490755,0.0297523943239435,0.04914758195234233,0.07274095995254451,0.09648298897602905,0.11473974448572152,0.12242290589566962,0.11730239306300665,0.10106472548951255,0.0784280466819872,0.05493705109838155,0.034831135820317584,0.020055344765853425,0.010529299858505377,0.0050656420543682724,0.0022490545528980853,9.337294613881614E-4,3.7414286514948444E-4,1.5653832618099035E-4,7.91850313298878E-5,5.4410065182970094E-5,4.858617856387561E-5,5.2279208997055236E-5,6.929451570507445E-5,1.1682474547506695E-4,2.3161824302679425E-4,4.7604362586885896E-4,9.338616719697029E-4,0.0016837755448831228,0.002747706553410417,0.00403301540376022,0.005310355129219929,0.006265512045295044,0.006620948298530703,0.006265512045293909,0.005310355129206017,0.004033015403608119,0.0027477065519208974,0.0016837755318104112,9.338615690880197E-4,4.7604289925583444E-4,2.3161363284574806E-4,1.1679843139604698E-4,6.91591524140494E-5,5.165020746917408E-5,4.593857029284479E-5,4.428233334211211E-5,4.385492033022727E-5,4.375667108614405E-5,4.373653943100977E-5,4.373286025184471E-5,4.373226025362682E-5,4.37321729068024E-5,4.3732161551865934E-5,4.3732160233359066E-5,4.3732160096573105E-5,4.373216008389225E-5,4.3732160082841555E-5,4.373216008276374E-5,4.373216008275857E-5,4.3732160082758275E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.3732160082758255E-5,4.37321600827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ENSMUST00000002320,-,949,1195,G701,Background,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.6482346950466264E-8,3.648234695046734E-8,3.648234695049004E-8,3.648234695091927E-8,3.648234695817788E-8,3.6482347067960276E-8,3.648234855293286E-8,3.648236651676563E-8,3.648256085870998E-8,3.6484441119625136E-8,3.650071000857255E-8,3.662660252303323E-8,3.7497910249040644E-8,4.289199754527567E-8,7.276694235695044E-8,2.2082628012165477E-7,8.776306748298256E-7,3.486672751323966E-6,1.277183826028166E-5,4.23946483550747E-5,1.2717473130855955E-4,3.4500293298137446E-4,8.477965885297867E-4,0.001890937670213247,0.003836414070628575,0.007096300332603122,0.01199640065044867,0.018584659375156007,0.02647058360829676,0.03481453967194997,0.042537510268435365,0.04868948909674047,0.052781118229236194,0.0548728989397386,0.05537245619774566,0.05469764761266365,0.053040003470330895,0.0503511256207974,0.046501182575827645,0.04148024902458134,0.03554510110532413,0.029260233068118768,0.02339610264922965,0.018682772340457718,0.015509763799891663,0.013743760531847051,0.012800828561764637,0.011953606852891662,0.010693723600612144,0.008936529308405446,0.006972339150662233,0.005235500405186318,0.004053002140084516,0.0035041683745114243,0.003428097526052157,0.003536314534072173,0.0035581876073489407,0.0033533516408769696,0.0029501610260143376,0.002504200307704329,0.002205900908070195,0.0021847405125587412,0.0024516743232778416,0.0029000034534090295,0.0033600802157876743,0.0036806621334421648,0.0037953791290262833,0.003738751315980289,0.0036065572308097015,0.0034910702454861004,0.0034335886851887924,0.0034165992106265893,0.003387677857561815,0.0032929553309733158,0.003103193177836782,0.002825423169258004,0.002497898587364509,0.0021699559348996368,0.0018763393684858823,0.001621756963861572,0.001386202499736801,0.0011461527954953537,8.947240897748908E-4,6.464916393408766E-4,4.2652996270121425E-4,2.547802934598295E-4,1.371029213263132E-4,6.627958163204872E-5,2.874562335067805E-5,1.1183730460339245E-5,3.9122359883178424E-6,1.2427885286792697E-6,3.7252882474616597E-7,1.202623663273348E-7,5.517442312585978E-8,4.0214309936381094E-8,3.714911111049789E-8,3.6588947142125886E-8,3.649759773117903E-8,3.648429936985289E-8,3.648257061662742E-8,3.6482369878833665E-8,3.648234905371862E-8,3.6482347123111584E-8,3.648234696314751E-8,3.648234695129974E-8,3.648234695051524E-8,3.648234695046879E-8,3.648234695046634E-8,3.6482346950466225E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.648234695046622E-8,3.6482346950466225E-8,3.648234695046634E-8,3.648234695046879E-8,3.648234695051525E-8,3.6482346951299884E-8,3.6482346963150596E-8,3.648234712317027E-8,3.6482349054715745E-8,3.648236989399223E-8,3.6482570822798526E-8,3.6484301878479275E-8,3.649762503704315E-8,3.658921300236143E-8,3.715142629196119E-8,4.023233994170791E-8,5.529997283426282E-8,1.2104391279206928E-7,3.7687690491919207E-7,1.2644004878533983E-6,4.008164773612918E-6,1.1563748299766648E-5,3.0088125922486065E-5,7.05044851368302E-5,1.4892974172056616E-4,2.841680616046953E-4,4.911558115425995E-4,7.716968561726708E-4,0.0011069034224529084,0.0014568504256608926,0.0017702552952173066,0.002001603483563199,0.002128268388396211,0.0021585749010362442,0.0021247263033005903,0.002062201031620192,0.00198692380815559,0.0018859896117941124,0.0017301608143794004,0.0014999163579703277,0.001205436651166092,8.858580098358377E-4,5.900567988845136E-4,3.5433166283608034E-4,1.912325640793043E-4,9.261384174432796E-5,4.0300707103273765E-5,1.6102951019123315E-5,7.148460118154172E-6,7.145814371360675E-6,1.6087582721915016E-5,4.02356138192611E-5,9.237219648773223E-5,1.9044598471798844E-4,3.5210573638265355E-4,5.84664741228872E-4,8.750222901993275E-4,0.0011887558846210113,0.0014859348409677023,0.001750121595029313,0.002012798960143948,0.002351558314280047,0.0028548553504229384,0.0035704837789186017,0.004468863263624035,0.005442748203435859,0.006340097552592284,0.00700833404193477,0.0073296097339220646,0.007240974259257356,0.006743465552878396,0.005902675630437866,0.004837796664247069,0.00369665199096065,0.002621520172106831,0.0017174309613590074,0.0010347319902638222,5.708786014788903E-4,2.872960693455473E-4,1.3142929086663004E-4,5.4499038443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/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/ReadGroup.java
public String displayConversionPercent() {
		double[] result = new double[(int) (_endPosition - _startPosition + 1)];
		long currentPosition = _startPosition;
		while( currentPosition <= _endPosition ) {
			if( _conversionMap.containsKey(currentPosition) ) {
				result[(int) (currentPosition - _startPosition)] =
					(double) _conversionMap.get(currentPosition) / (double) _countMap.get(currentPosition);
			}
			else { result[(int) (currentPosition - _startPosition)] = -1.0; }
			currentPosition++;
		}
		
		return join(result);
	}	

#@
private static String _conversion = "T>C";
/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1_src/PARCLIPbowtieParser.java
		Pattern crosslinkPattern = Pattern.compile("^(\\d+):"+conversion+"$");
	private static final Transliteration _oppositeStrandTransliterate = Transliteration.compile("ACGT", "TGCA");
...
String mismatchInfo[] = lineArray[7].split(",");
				for( String currentMismatch : mismatchInfo ) {
					String currentMismatchCrosslink = currentMismatch;
					if( strand == '-' ) {
						currentMismatchCrosslink = _oppositeStrandTransliterate.translate(currentMismatchCrosslink); 
					}		
					Matcher match = crosslinkPattern.matcher( currentMismatchCrosslink );
					if( match.find() ) {
						if( strand == '+' ) {
							conversionLocations.put( Byte.valueOf(match.group(1)), readCount);
						}
						else {
							conversionLocations.put( Byte.valueOf(Integer.toString(lineArray[4].length() - 1 - Integer.parseInt(match.group(1)))), readCount);
						}
					}
					else {
						mismatchCount++;
					}
				}