/***************************************************************************** # Copyright (C) 1994-2008 by David Gordon. # All rights reserved. # # This software is part of a beta-test version of the Consed/Autofinish # package. It should not be redistributed or # used for any commercial purpose, including commercially funded # sequencing, without written permission from the author and the # University of Washington. # # This software is provided ``AS IS'' and any express or implied # warranties, including, but not limited to, the implied warranties of # merchantability and fitness for a particular purpose, are disclaimed. # In no event shall the authors or the University of Washington be # liable for any direct, indirect, incidental, special, exemplary, or # consequential damages (including, but not limited to, procurement of # substitute goods or services; loss of use, data, or profits; or # business interruption) however caused and on any theory of liability, # whether in contract, strict liability, or tort (including negligence # or otherwise) arising in any way out of the use of this software, even # if advised of the possibility of such damage. # # Building Consed from source is error prone and not simple which is # why I provide executables. Due to time limitations I cannot # provide any assistance in building Consed. Even if you do not # modify the source, you may introduce errors due to using a # different version of the compiler, a different version of motif, # different versions of other libraries than I used, etc. For this # reason, if you discover Consed bugs, I can only offer help with # those bugs if you first reproduce those bugs with an executable # provided by me--not an executable you have built. # # Modifying Consed is also difficult. Although Consed is modular, # some modules are used by many other modules. Thus making a change # in one place can have unforeseen effects on many other features. # It may takes months for you to notice these other side-effects # which may not seen connected at all. It is not feasable for me to # provide help with modifying Consed sources because of the # potentially huge amount of time involved. # #*****************************************************************************/ // // lowconsqual.cpp // // Implementation for LowConsQualTagList class. // // chrisa 13-mar-95 // #include "sysdepend.h" #include "lowconsqual.h" #include "consedParameters.h" // this is the description string given to each individual // gotoItem's reason static const char* szGotoItemDesc = "base quality below threshold"; // ctor reads through consensus of passed contig, adds a // gotoItem to list each time it encounters a region where // quality is <= ucQualityLow (as defined by quality.h) LowConsQualGotoList::LowConsQualGotoList(Contig* pContig) { int nQualityThreshold = consedParameters::pGetConsedParameters()->nQualityThresholdForLowConsensusQuality_; int nEnd, nStart; bool bHaveGotoItem = false; for (int n = pContig->nGetStartConsensusIndex(); n <= pContig->nGetEndConsensusIndex(); n++) { //cout << "testing quality at " << n << ": consensus = " << //(*pContig)[n] << endl; //cout.flush(); // ignore pads Ntide nt = pContig->ntGetCons(n); if ( ! nt.bIsPad() ) { // test for low quality base if ( (nt.qualGetQuality() <= nQualityThreshold ) || (nt.qualGetQuality() == ucQualityLowEdited) ) { // this consensus base is of low quality. build a gotoItem if (bHaveGotoItem) { // one already in progress. extend region. nEnd = n; } else { // start a new gotoItem bHaveGotoItem = true; nStart = n; nEnd = n; } } else { // base of high(er) quality. was there a gotoItem in progress? // if so, add the gotoItem and clear bHaveGotoItem if (bHaveGotoItem) { gotoItem* pGotoItem = new gotoItem(pContig, NULL, // no fragment nStart, // fix me !!!!!! nEnd, // fix me !!!!!! pContig->nUnpaddedIndex(nStart), pContig->nUnpaddedIndex(nEnd), szGotoItemDesc); addToList(pGotoItem); bHaveGotoItem = false; } } // base was of higher quality } // base was not a pad } // for loop // any left over at end (probably so)? if (bHaveGotoItem) { gotoItem* pGotoItem = new gotoItem(pContig, NULL, // no fragment nStart, // fix me !!!!!! nEnd, // fix me !!!!!! pContig->nUnpaddedIndex(nStart), pContig->nUnpaddedIndex(nEnd), szGotoItemDesc); addToList(pGotoItem); } } // LowConsQualGotoList ctor