v1 - Revision 103831: /trunk/c++/src/app/oligofar

• ..
• Changes
• Makefile.align.app
• Makefile.app
• Makefile.bmfilter.app
• Makefile.fadice.app
• Makefile.in
• Makefile.oligofar.app
• Makefile.testsamrecord.app
• Makefile.wbmask.app
• Problems.txt
• README.build
• README.txt
• align-main.cpp
• aligners.hpp
• aoutputformatter.cpp
• aoutputformatter.hpp
• array_map.hpp
• array_set.hpp
• bmfilter-main.cpp
• bmtagger.sh
• caligner-align.cpp
• caligner-aligndiag.cpp
• caligner-aligntail.cpp
• caligner-aligntaildiag.cpp
• caligner-alignwindow.cpp
• caligner-alignwintwodiag.cpp
• caligner.cpp
• caligner.hpp
• calignerbase.cpp
• calignerbase.hpp
• calignparam.hpp
• caligntest.cpp
• caligntest.hpp
• capp.cpp
• capp.hpp
• cbatch.cpp
• cbatch.hpp
• cbithacks.hpp
• cbitmaskaccess.cpp
• cbitmaskaccess.hpp
• cbitmaskbase.hpp
• cbitmaskbuilder.cpp
• cbitmaskbuilder.hpp
• cfadiceapp.cpp
• cfadiceapp.hpp
• cfeatmap.hpp
• cfilter.cpp
• cfilter.hpp
• cgetopt.hpp
• cguidefile.cpp
• cguidefile.hpp
• cguidesam.cpp
• cguidesam.hpp
• chashatom.hpp
• chashparam.hpp
• chashpopulator.hpp
• chit.cpp
• chit.hpp
• cintron.hpp
• coligofarapp-aligners.cpp
• coligofarapp-tests.cpp
• coligofarapp.cpp
• coligofarapp.hpp
• coligofarcfg.cpp
• coligofarcfg.hpp
• coutputformatter.cpp
• coutputformatter.hpp
• cpassparam.hpp
• cpermutator8b.cpp
• cpermutator8b.hpp
• cprogressindicator.cpp
• cprogressindicator.hpp
• cquery.cpp
• cquery.hpp
• cqueryhash.cpp
• cqueryhash.hpp
• creadtagger.cpp
• creadtagger.hpp
• csam.hpp
• csamalignments.cpp
• csamalignments.hpp
• csamformatter.cpp
• csamformatter.hpp
• csammdformatter.cpp
• csammdformatter.hpp
• csamrecords.cpp
• csamrecords.hpp
• cscancallback.hpp
• cscore-impl.cpp
• cscore-impl.hpp
• cscoreparam.hpp
• cscoretbl.cpp
• cscoretbl.hpp
• cscoring.cpp
• cscoring.hpp
• cscoringfactory.hpp
• cseqbuffer.hpp
• cseqcoding.cpp
• cseqcoding.hpp
• cseqids.hpp
• cseqscanner.cpp
• cseqscanner.hpp
• cseqvecprocessor.hpp
• cshortreader.cpp
• cshortreader.hpp
• csnpdb.cpp
• csnpdb.hpp
• cspacialranges.hpp
• ctranscript.hpp
• cwordhash.hpp
• daligner.hpp
• debug.hpp
• defs.hpp
• dust.hpp
• fadice-main.cpp
• fourplanes.hpp
• getopt.c
• getopt.h
• ialigner.hpp
• ialignmentmap.hpp
• iguidefile.hpp
• ioutputformatter.hpp
• iprogress.hpp
• iscore.hpp
• main.cpp
• man/
• oligofar-version.hpp
• scopes.hpp
• string-util.hpp
• subjectwmask-main.cpp
• taligner_fast.hpp
• taligner_hsp.hpp
• taligner_sw.hpp
• talignerbase.hpp
• tests/
• testsamrecords.cpp
• tseqref.hpp
• types.hpp
• uinth.hpp
• util.cpp
• util.hpp