| /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;
|