New upstream version 3.02b
Andreas Tille
7 years ago
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Full instructions for installing and running Glimmer are in file
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glim302notes.pdf in this directory.
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Here's a quick start guide for the inpatient:
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- To build all Glimmer programs, go to the src directory and type make
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(or alternately gmake). This will create all the executable files
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in the directory bin. Note that initially directories bin, lib and
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obj are all empty.
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- Scripts for running the programs are in directory scripts. Each
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needs to be edited near the top to specify the correct location
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(give the full path) where you have the bin and scripts directories
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on your system. Script g3-iterated.csh is generally the best to use
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to make gene predictions from a single genome sequence without other
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data.
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- Some scripts (including g3-iterated.csh) use the program elph, which
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needs to be separately downloaded and installed. You can get it from
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ccb.jhu.edu/software/ELPH/index.shtml
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- Help on options and command parameters for each program can be gotten
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by running the program with a -h option.
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#include <iomanip>
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30 | 30 |
#include <fstream>
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#include <vector>
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#include <string>
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#include <cstring>
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33 | 33 |
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#include "exceptions.hh"
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35 | 35 |
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530 | 530 |
if (p == NULL)
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531 | 531 |
return;
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532 | 532 |
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for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
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q -> disqualified = true;
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// Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
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// whose pos might be >= cutoff
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for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
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q = q -> best_pred)
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{
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if (cutoff <= q -> pos)
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q -> disqualified = true;
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}
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535 | 541 |
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536 | 542 |
return;
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537 | 543 |
}
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2660 | 2666 |
if (p == NULL)
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2661 | 2667 |
return;
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2662 | 2668 |
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for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
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q -> disqualified = false;
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// Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
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// whose pos might be >= cutoff
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for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
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q = q -> best_pred)
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{
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if (cutoff <= q -> pos)
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q -> disqualified = false;
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}
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2665 | 2677 |
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2666 | 2678 |
return;
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2667 | 2679 |
}
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29 | 29 |
#include <iomanip>
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30 | 30 |
#include <fstream>
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#include <vector>
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#include <string>
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#include <cstring>
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33 | 33 |
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#include "exceptions.hh"
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35 | 35 |
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530 | 530 |
if (p == NULL)
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531 | 531 |
return;
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532 | 532 |
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for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
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q -> disqualified = true;
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// Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
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// whose pos might be >= cutoff
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for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
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q = q -> best_pred)
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{
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if (cutoff <= q -> pos)
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q -> disqualified = true;
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}
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535 | 541 |
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536 | 542 |
return;
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537 | 543 |
}
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2660 | 2666 |
if (p == NULL)
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2661 | 2667 |
return;
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2662 | 2668 |
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for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
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q -> disqualified = false;
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// Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
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// whose pos might be >= cutoff
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for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
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q = q -> best_pred)
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{
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if (cutoff <= q -> pos)
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q -> disqualified = false;
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}
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2665 | 2677 |
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2666 | 2678 |
return;
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2667 | 2679 |
}
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