Package list tigr-glimmer / eb1b8e5
New upstream version 3.02b Andreas Tille 4 years ago
9 changed file(s) with 63 addition(s) and 16 deletion(s). Raw diff Collapse all Expand all
0 Full instructions for installing and running Glimmer are in file
1 glim302notes.pdf in this directory.
2
3 Here's a quick start guide for the inpatient:
4
5 - To build all Glimmer programs, go to the src directory and type make
6 (or alternately gmake). This will create all the executable files
7 in the directory bin. Note that initially directories bin, lib and
8 obj are all empty.
9
10 - Scripts for running the programs are in directory scripts. Each
11 needs to be edited near the top to specify the correct location
12 (give the full path) where you have the bin and scripts directories
13 on your system. Script g3-iterated.csh is generally the best to use
14 to make gene predictions from a single genome sequence without other
15 data.
16
17 - Some scripts (including g3-iterated.csh) use the program elph, which
18 needs to be separately downloaded and installed. You can get it from
19 ccb.jhu.edu/software/ELPH/index.shtml
20
21 - Help on options and command parameters for each program can be gotten
22 by running the program with a -h option.
2929 #include <iomanip>
3030 #include <fstream>
3131 #include <vector>
32 #include <string>
32 #include <cstring>
3333
3434 #include "exceptions.hh"
3535
259259 // Print the contents of this PWM to fp .
260260
261261 {
262 char * tag = "acgt";
262 const char * tag = "acgt";
263263 int width;
264264 int i, j;
265265
442442 // Return a subscript corresponding to character ch .
443443
444444 {
445 char * p;
445 const char * p;
446446
447447 p = strchr (CONVERSION_STRING, tolower (ch));
448448 if (p == NULL)
530530 if (p == NULL)
531531 return;
532532
533 for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
534 q -> disqualified = true;
533 // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
534 // whose pos might be >= cutoff
535 for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
536 q = q -> best_pred)
537 {
538 if (cutoff <= q -> pos)
539 q -> disqualified = true;
540 }
535541
536542 return;
537543 }
26602666 if (p == NULL)
26612667 return;
26622668
2663 for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
2664 q -> disqualified = false;
2669 // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
2670 // whose pos might be >= cutoff
2671 for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
2672 q = q -> best_pred)
2673 {
2674 if (cutoff <= q -> pos)
2675 q -> disqualified = false;
2676 }
26652677
26662678 return;
26672679 }
19801980 // model) for character ch .
19811981
19821982 {
1983 char * p;
1983 const char * p;
19841984
19851985 p = strchr (ALPHA_STRING, tolower (Filter (ch)));
19861986 if (p == NULL)
2929 #include <iomanip>
3030 #include <fstream>
3131 #include <vector>
32 #include <string>
32 #include <cstring>
3333
3434 #include "exceptions.hh"
3535
259259 // Print the contents of this PWM to fp .
260260
261261 {
262 char * tag = "acgt";
262 const char * tag = "acgt";
263263 int width;
264264 int i, j;
265265
442442 // Return a subscript corresponding to character ch .
443443
444444 {
445 char * p;
445 const char * p;
446446
447447 p = strchr (CONVERSION_STRING, tolower (ch));
448448 if (p == NULL)
530530 if (p == NULL)
531531 return;
532532
533 for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
534 q -> disqualified = true;
533 // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
534 // whose pos might be >= cutoff
535 for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
536 q = q -> best_pred)
537 {
538 if (cutoff <= q -> pos)
539 q -> disqualified = true;
540 }
535541
536542 return;
537543 }
26602666 if (p == NULL)
26612667 return;
26622668
2663 for (q = p -> best_pred; q != NULL && cutoff <= q -> pos; q = q -> best_pred)
2664 q -> disqualified = false;
2669 // Search to cutoff - Max_Olap_Bases to make sure we reach all nodes
2670 // whose pos might be >= cutoff
2671 for (q = p -> best_pred; q != NULL && cutoff - Max_Olap_Bases <= q -> pos;
2672 q = q -> best_pred)
2673 {
2674 if (cutoff <= q -> pos)
2675 q -> disqualified = false;
2676 }
26652677
26662678 return;
26672679 }
19801980 // model) for character ch .
19811981
19821982 {
1983 char * p;
1983 const char * p;
19841984
19851985 p = strchr (ALPHA_STRING, tolower (Filter (ch)));
19861986 if (p == NULL)