/dports/biology/bbmap/bbmap/current/pacbio/ |
H A D | RemoveAdapters3.java | 254 ALIGN_COLUMNS=Tools.max(window, rcompDistance)+5; in ProcessThread() 257 assert(window<ALIGN_COLUMNS); in ProcessThread() 259 msa=new MultiStateAligner9PacBioAdapter(ALIGN_ROWS, ALIGN_COLUMNS); in ProcessThread() 260 …msaR=new MultiStateAligner9PacBio(ALIGN_ROWS, ALIGN_COLUMNS); //TODO: Why is this not 'adapter' ve… in ProcessThread() 538 private final int ALIGN_COLUMNS;
|
H A D | RemoveAdapters2.java | 276 ALIGN_COLUMNS=ALIGN_ROWS*3+20; in ProcessThread() 281 assert(window<ALIGN_COLUMNS); in ProcessThread() 283 msa=new MultiStateAligner9PacBioAdapter(ALIGN_ROWS, ALIGN_COLUMNS); in ProcessThread() 582 private final int ALIGN_COLUMNS;
|
/dports/biology/bbmap/bbmap/current/var/ |
H A D | GenerateVarlets3.java | 94 ALIGN_COLUMNS=Integer.parseInt(b); in main() 759 …new MultiStateAligner9PacBio(ALIGN_ROWS, ALIGN_COLUMNS) : new MultiStateAligner9ts(ALIGN_ROWS, AL… 848 public static int ALIGN_COLUMNS=3000; local
|
H A D | GenerateVarlets.java | 611 …new MultiStateAligner9ts(ALIGN_ROWS, ALIGN_COLUMNS) : new MultiStateAligner9ts(ALIGN_ROWS, ALIGN_… 652 public static int ALIGN_COLUMNS=3000; local
|
H A D | GenerateVarlets2.java | 562 …new MultiStateAligner9ts(ALIGN_ROWS, ALIGN_COLUMNS) : new MultiStateAligner9ts(ALIGN_ROWS, ALIGN_… 640 public static int ALIGN_COLUMNS=3000; field in GenerateVarlets2
|
/dports/biology/ncbi-toolkit/ncbi/object/ |
H A D | objalignloc.c | 1111 atp = AsnReadId(aip, amp, ALIGN_COLUMNS); in AlignColumnsAsnRead() 1113 atp = AsnLinkType(orig, ALIGN_COLUMNS); in AlignColumnsAsnRead() 1186 atp = AsnLinkType(orig, ALIGN_COLUMNS); /* link local tree */ in AlignColumnsAsnWrite()
|
H A D | alignloc.h | 165 #define ALIGN_COLUMNS &at[30] macro
|
/dports/biology/bbmap/bbmap/current/align2/ |
H A D | BBMapThread5.java | 26 static final int ALIGN_COLUMNS=BBIndex5.ALIGN_COLUMNS; field in BBMapThread5 65 public final int ALIGN_COLUMNS(){return ALIGN_COLUMNS;} in ALIGN_COLUMNS() method in BBMapThread5
|
H A D | BBMapThreadPacBio.java | 26 static final int ALIGN_COLUMNS=BBIndexPacBio.ALIGN_COLUMNS; field in BBMapThreadPacBio 66 public final int ALIGN_COLUMNS(){return ALIGN_COLUMNS;} in ALIGN_COLUMNS() method in BBMapThreadPacBio
|
H A D | BBMapThread.java | 26 static final int ALIGN_COLUMNS=BBIndex.ALIGN_COLUMNS; field in BBMapThread 69 public final int ALIGN_COLUMNS(){return ALIGN_COLUMNS;} in ALIGN_COLUMNS() method in BBMapThread
|
H A D | BBMapThreadAcc.java | 26 static final int ALIGN_COLUMNS=BBIndexAcc.ALIGN_COLUMNS; field in BBMapThreadAcc 69 public final int ALIGN_COLUMNS(){return ALIGN_COLUMNS;} in ALIGN_COLUMNS() method in BBMapThreadAcc
|
H A D | BBMapThreadPacBioSkimmer.java | 27 static final int ALIGN_COLUMNS=BBIndexPacBioSkimmer.ALIGN_COLUMNS; field in BBMapThreadPacBioSkimmer 74 public final int ALIGN_COLUMNS(){return ALIGN_COLUMNS;} in ALIGN_COLUMNS() method in BBMapThreadPacBioSkimmer
|
H A D | AbstractMapThread.java | 95 …EXPECTED_LEN_LIMIT=(ALIGN_COLUMNS()*17)/20-(2*(SLOW_ALIGN_PADDING+10)); //TODO: Due to some bug in… in AbstractMapThread() 97 ALIGN_COLUMNS_ABSTRACT=ALIGN_COLUMNS(); in AbstractMapThread() 137 msa=MSA.makeMSA(ALIGN_ROWS(), ALIGN_COLUMNS(), MSA_TYPE); in AbstractMapThread() 170 public abstract int ALIGN_COLUMNS(); in ALIGN_COLUMNS() method in AbstractMapThread
|
H A D | BBIndexPacBioSkimmer.java | 2138 public static final int ALIGN_COLUMNS=5500;
|
H A D | BBIndex5.java | 2501 public static final int ALIGN_COLUMNS=3000; local
|
H A D | BBIndexPacBio.java | 2474 public static final int ALIGN_COLUMNS=7600; field in BBIndexPacBio
|
H A D | BBIndexAcc.java | 2669 public static final int ALIGN_COLUMNS=3000; local
|
H A D | BBIndex.java | 3195 public static final int ALIGN_COLUMNS=3000; local
|
/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamFinder.java | 135 ALIGN_COLUMNS=window+2; in IceCreamFinder() 1591 …apter || trimReads) ? new SingleStateAlignerPacBioAdapter(ALIGN_ROWS, ALIGN_COLUMNS, adapter.lengt… 1777 protected final int ALIGN_COLUMNS;
|