recon: new package at 1.08 (#11408)
* recon: new package at 1.08 * recon: add period * recon: use proper decorators, better documentation * recon: fix incorrect os import * recon: add repeatmasker patch as variant
This commit is contained in:
Justin S
Levi Baber
parent
80d7573df8
commit
62fa813678
2 changed files with 635 additions and 0 deletions
52
var/spack/repos/builtin/packages/recon/package.py
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52
var/spack/repos/builtin/packages/recon/package.py
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@ -0,0 +1,52 @@
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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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from os import symlink
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class Recon(MakefilePackage):
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"""RECON: a package for automated de novo identification of repeat families
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from genomic sequences."""
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homepage = "http://eddylab.org/software/recon/"
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url = "http://eddylab.org/software/recon/RECON1.05.tar.gz"
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version('1.05', sha256='4d4f76f439bcffd50380cffc41a80dc15fa4a80f38a04234e24da893ed7c025a')
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variant('repeatmasker', default=False,
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description='Use RepeatMasker developer patches (1.08)')
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patch('repeatmasker_recon.patch', when='+repeatmasker')
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build_directory = 'src'
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depends_on('perl', type='run')
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@property
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def install_targets(self):
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return [
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'install',
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'BINDIR=%s' % self.prefix.bin
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]
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# edit the recon.pl script with the prefix as mentioned in the README
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def edit(self, spec, prefix):
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filter_file('$path = ""', '$path = "%s"' % prefix.bin,
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'scripts/recon.pl', string=True)
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# recon's makefile is very basic -- the target directory must
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# already exist to properly install
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@run_before('install')
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def prepare_bin(self):
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mkdirp(prefix.bin)
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# finally, install the scripts dir as well
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# and link the recon command into bin.
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@run_after('install')
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def finalize(self):
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install_tree('scripts', prefix.scripts)
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symlink(join_path(prefix.scripts, 'recon.pl'),
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join_path(prefix.bin, 'recon'))
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583
var/spack/repos/builtin/packages/recon/repeatmasker_recon.patch
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583
var/spack/repos/builtin/packages/recon/repeatmasker_recon.patch
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@ -0,0 +1,583 @@
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diff -ruN RECON1.05/00README RECON-1.08/00README
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--- RECON1.05/00README 2002-04-08 14:31:59.000000000 -0500
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+++ RECON-1.08/00README 2014-02-05 16:05:18.000000000 -0600
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@@ -1,6 +1,7 @@
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RECON -- finding repeat families from biological sequences
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-Version 1.03 (Mar 2002)
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+Version 1.08 (Jan 2014)
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Copyright (C) 2001 Washington University School of Medicine
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+Copyright (C) 2011-2014 Institute for Systems Biology
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------------------------------------------------------------------
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@@ -28,8 +29,26 @@
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What's new?
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+RECON1.08: Wed Feb 5 14:04:25 PST 2014 - Robert Hubley ISB
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+ - New checks in eleredef.c for failed memory allocation/file operations.
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+ - A buffer overrun bug fix provided by Stephen Ficklin in eledef.c.
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+
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+RECON1.07: Wed Jun 8 10:00:55 PDT 2011 - Robert Hubley ISB
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+ - Another problem with the eleredef program has appeared a couple
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+ of times. A divide by zero error in one of Zhirong's routines.
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+ I have applied a workaround to the divide by zero but not a fix
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+ to the real problem. The program will now warn the user if
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+ the workaround was exercised during a run.
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+
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+RECON1.06: Tue May 20 15:19:30 PDT 2008 - Robert Hubley ISB
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+ - 64 bit compiler fixes: Previous versions of RECON used the "long"
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+ data type under the assumption that was 32bits. This caused the
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+ program to crash or lock up during analysis.
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+
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Bug fix for RECON1.02 in the eleredef program.
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+
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+
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Programs and input
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The RECON algorithm defines repeat families on the basis of pairwise
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@@ -50,7 +69,6 @@
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multiple times and concatenate the result into one MSP file.
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-
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The recon script drives the running of the package. The command
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line format is as follows:
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diff -ruN RECON1.05/src/bolts.h RECON-1.08/src/bolts.h
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--- RECON1.05/src/bolts.h 2002-01-10 15:19:09.000000000 -0600
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+++ RECON-1.08/src/bolts.h 2014-02-05 16:05:18.000000000 -0600
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@@ -10,5 +10,5 @@
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-long seq_no;
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+int32_t seq_no;
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char **seq_names;
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diff -ruN RECON1.05/src/edgeredef.c RECON-1.08/src/edgeredef.c
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--- RECON1.05/src/edgeredef.c 2002-07-19 10:42:03.000000000 -0500
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+++ RECON-1.08/src/edgeredef.c 2014-02-05 16:05:18.000000000 -0600
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@@ -58,6 +58,10 @@
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}
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log_file = fopen("tmp2/log", "w");
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+ if (!log_file) {
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+ printf("Can not open log_file. Exiting\n");
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+ exit(1);
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+ }
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while (fgets(line, 15, ele_no)) {
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ele_ct = atoi(line);
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@@ -191,7 +195,7 @@
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} else {
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ele_info->stat = 'y';
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ele_cleanup(&ele_info->ele);
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- command = (char *) malloc(30*sizeof(char));
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+ command = (char *) malloc(80*sizeof(char));
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sprintf(command, "cp tmp/e%d tmp2/.", ele_info->index);
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system(command);
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free(command);
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diff -ruN RECON1.05/src/eledef.c RECON-1.08/src/eledef.c
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--- RECON1.05/src/eledef.c 2002-01-10 15:19:10.000000000 -0600
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+++ RECON-1.08/src/eledef.c 2014-02-05 16:05:18.000000000 -0600
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@@ -385,7 +385,7 @@
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void img_charge(IPROT_t **shadow, int ct, FILE *input) {
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int i=0, pos=0;
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- char line[100];
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+ char line[151];
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int scan_flag;
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MSP_t msp;
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diff -ruN RECON1.05/src/ele.h RECON-1.08/src/ele.h
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--- RECON1.05/src/ele.h 2002-01-10 15:19:09.000000000 -0600
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+++ RECON-1.08/src/ele.h 2014-02-05 16:05:18.000000000 -0600
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@@ -1,7 +1,6 @@
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#include "msps.h"
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-
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#define SIZE_LIMIT 500
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#define TANDEM 5
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@@ -9,13 +8,13 @@
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typedef struct cp_list {
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- long cp;
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+ int32_t cp;
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struct ele_info *contributor;
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struct cp_list *next;
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} CP_t;
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typedef struct bd_list {
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- long bd;
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+ int32_t bd;
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int support;
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struct bd_list *next;
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} BD_t;
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@@ -24,7 +23,7 @@
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int index;
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char type; /* 'p', 's', 'c' */
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int direction; /* for clustering elements in consistent directions */
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- long score; /* for edge_filt, to solve the PPS problem */
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+ int32_t score; /* for edge_filt, to solve the PPS problem */
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struct ele_info *ele1_info, *ele2_info;
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} EDGE_t;
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@@ -67,6 +66,7 @@
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struct ele_list *next;
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} ELE_DATA_t;
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+
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typedef struct family {
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int index;
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char name[10];
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@@ -139,21 +139,45 @@
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void frag_data_free(FRAG_DATA_t **);
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void frag_data_cleanup(FRAG_DATA_t **);
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-
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+void print_ele_info(ELE_INFO_t *rt);
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+void print_ele_data(ELE_DATA_t *rt);
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/*MSP_DATA_t *all_msps=NULL;
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EDGE_t *efav=NULL;*/
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ELE_INFO_t **all_ele;
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int ele_ct, ele_array_size, fam_ct;
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int clan_size, clan_core_size;
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-long msp_in_mem, msp_left, msp_ct, msp_index;
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-long edge_index, edge_in_mem, edge_left, edge_ct;
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-long files_read, clan_ct, err_no;
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+int32_t msp_in_mem, msp_left, msp_ct, msp_index;
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+int32_t edge_index, edge_in_mem, edge_left, edge_ct;
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+int32_t files_read, clan_ct, err_no;
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ELE_INFO_t *ele_info_data, *ele_info_tail;
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FAM_DATA_t *FAMs;
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FILE *err, *new_msps, *eles, *unproc, *combo, *obs, *fams, *log_file;
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+/***************
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+ * DEBUG *
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+ ***************/
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+
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+void print_ele_data(ELE_DATA_t *rt) {
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+ if (!rt) return;
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+ print_ele_info( rt->ele_info );
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+ if (rt->next)
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+ print_ele_data(rt->next);
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+}
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+
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+void print_ele_info(ELE_INFO_t *rt) {
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+ if (!rt) return;
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+ printf("ele: index=%d, stat=%c, file_update=%d", rt->index, rt->stat,
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+ rt->file_updated );
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+ if ( rt->to_family )
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+ printf(" family_index=%d,", rt->to_family->index );
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+ if ( rt->ele )
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+ printf(" ele_index=%d", rt->ele->index );
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+ else
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+ printf(" ele=NULL");
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+ printf("\n");
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+}
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@@ -1341,7 +1365,7 @@
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-
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+/* Unused */
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void msp_data_free(MSP_DATA_t **md) {
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MSP_DATA_t *cur, *next;
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diff -ruN RECON1.05/src/eleredef.c RECON-1.08/src/eleredef.c
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--- RECON1.05/src/eleredef.c 2002-03-22 14:01:54.000000000 -0600
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+++ RECON-1.08/src/eleredef.c 2014-02-05 16:05:18.000000000 -0600
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@@ -51,7 +51,7 @@
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BD_t *CP_cluster(CP_t *);
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void CP_sort(CP_t **);
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void BD_sort(BD_t **);
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-int span(ELEMENT_t *, long);
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+int span(ELEMENT_t *, int32_t);
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void TBD_merge(ELEMENT_t *);
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void dissect(ELE_INFO_t *);
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@@ -67,16 +67,16 @@
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void edges_and_cps(ELE_INFO_t *, IMAGE_t **);
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int full_length(IMAGE_t *, float);
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-void add_CP(CP_t **, long, ELE_INFO_t *);
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-void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, long, short);
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+void add_CP(CP_t **, int32_t, ELE_INFO_t *);
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+void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, int32_t, short);
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void adjust_edge_tree(ELE_INFO_t *);
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int charge_edge_array(EDGE_t **, EDGE_TREE_t *, int);
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int consis_tree_build(IMG_NODE_t *, IMAGE_t *, int);
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int consis(IMAGE_t *, IMAGE_t *, float);
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IMG_NODE_t **node_entry(IMG_NODE_t **);
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void consis_tree_free(IMG_NODE_t *);
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-/*int find_prim(struct img_node *, float, long, long, short, long *, short *);*/
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-int find_prim(IMG_NODE_t *, float, long, long, long, long, long, long, long, int *, long *, short *);
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+/*int find_prim(struct img_node *, float, int32_t, int32_t, short, int32_t *, short *);*/
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+int find_prim(IMG_NODE_t *, float, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int *, int32_t *, short *);
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void combo_output(ELE_INFO_t *);
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void obs_output(ELE_INFO_t *);
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@@ -90,9 +90,6 @@
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-
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-
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-
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int main (int argc, char *argv[]) {
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ELE_INFO_t *cur_ele_info;
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int i, ele_march, ei, rounds=0, start;
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@@ -125,7 +122,6 @@
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printf("Can not open naive_ele_no. Exiting\n");
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exit(1);
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}
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-
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msp_no = fopen("summary/redef_msp_no", "r");
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if (!msp_no) msp_no = fopen("summary/ori_msp_no", "r");
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if (!msp_no) {
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@@ -133,15 +129,46 @@
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exit(1);
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}
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+ // May or may not exist. All uses of edge_no first check for
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+ // its existence.
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edge_no = fopen("summary/naive_edge_no", "r");
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+
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+ // May or may not exist. All uses are checked.
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size_list = fopen("tmp/size_list", "r");
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+
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+ // May or may not exist. All uses are checked.
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new_stat = fopen("tmp2/redef_stat", "r");
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new_msps = fopen("summary/new_msps", "a");
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+ if ( !new_msps )
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+ {
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+ printf("Can not open summary/new_msps for writing! Exiting\n");
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+ exit(1);
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+ }
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unproc = fopen("summary/unproc", "a");
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+ if ( !unproc )
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+ {
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+ printf("Can not open summary/unproc for writing! Exiting\n");
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+ exit(1);
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+ }
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combo = fopen("summary/combo", "a");
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+ if ( !combo )
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+ {
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+ printf("Can not open summary/combo for writing! Exiting\n");
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+ exit(1);
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+ }
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obs = fopen("summary/obsolete", "a");
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+ if ( !obs )
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+ {
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+ printf("Can not open summary/obsolete for writing! Exiting\n");
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+ exit(1);
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+ }
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log_file = fopen("tmp2/log", "a");
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+ if ( !log_file )
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+ {
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+ printf("Can not open tmp2/log for writing! Exiting\n");
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+ exit(1);
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+ }
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while (fgets(line, 15, ele_no)) {
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ele_ct = atoi(line);
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@@ -170,7 +197,7 @@
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if (size_list && !new_stat) outthrow_big_tandems(size_list);
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fclose(unproc);
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|
|
||||||
|
- /* set file_updated for ele_info's */
|
||||||
|
+ /* set file_updated / stat for ele_info's */
|
||||||
|
if (new_stat) {
|
||||||
|
ele_ct = 0;
|
||||||
|
while (fgets(line, 35, new_stat)) {
|
||||||
|
@@ -207,6 +234,12 @@
|
||||||
|
/* re-define elements using the syntopy algorithm, and build edges */
|
||||||
|
img_ptr = (IMAGE_t **) malloc(MAX_IMG*sizeof(IMAGE_t *));
|
||||||
|
|
||||||
|
+ if ( ! img_ptr )
|
||||||
|
+ {
|
||||||
|
+ printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) );
|
||||||
|
+ exit(-1);
|
||||||
|
+ }
|
||||||
|
+
|
||||||
|
to_march = 1;
|
||||||
|
while (to_march) {
|
||||||
|
to_march = 0;
|
||||||
|
@@ -529,6 +562,11 @@
|
||||||
|
fprintf(log_file, "new clan: %d for ele %d\n", clan_ct, ele_info->index);
|
||||||
|
fflush(log_file);
|
||||||
|
build_local_network(ele_info, &local_net, &local_net_tail, img_ptr);
|
||||||
|
+ if ( ele_info->index == 362 || ele_info->index == 10 )
|
||||||
|
+ {
|
||||||
|
+ printf("Printing local net for 362\n");
|
||||||
|
+ print_ele_data( local_net );
|
||||||
|
+ }
|
||||||
|
fprintf(log_file, "clan size: %d, clan core size: %d\n", clan_size, clan_core_size);
|
||||||
|
fflush(log_file);
|
||||||
|
/* redefining elements in the local network */
|
||||||
|
@@ -1136,7 +1174,7 @@
|
||||||
|
|
||||||
|
#if 0
|
||||||
|
BD_t *CP_cluster(CP_t *cps) {
|
||||||
|
- long first = cps->cp, last = cps->cp, sum = 0;
|
||||||
|
+ int32_t first = cps->cp, last = cps->cp, sum = 0;
|
||||||
|
int cpct = 0;
|
||||||
|
BD_t *bds = NULL, *bd_tmp;
|
||||||
|
|
||||||
|
@@ -1171,7 +1209,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
BD_t *CP_cluster(CP_t *cps) {
|
||||||
|
- long first = cps->cp, last = cps->cp, sum = 0;
|
||||||
|
+ int32_t first = cps->cp, last = cps->cp, sum = 0;
|
||||||
|
CP_t *begin = cps;
|
||||||
|
int cpct = 0;
|
||||||
|
BD_t *bds = NULL, *bd_tmp;
|
||||||
|
@@ -1276,7 +1314,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-int span(ELEMENT_t *ele, long cut) {
|
||||||
|
+int span(ELEMENT_t *ele, int32_t cut) {
|
||||||
|
/* span requires PCP sorted according to cp_cmp and images sorted according to frag_cmp */
|
||||||
|
int left=0, rite=0;
|
||||||
|
IMG_DATA_t *id;
|
||||||
|
@@ -1348,18 +1386,20 @@
|
||||||
|
dissected = 0;
|
||||||
|
img_partner = partner(cur_img_data->to_image);
|
||||||
|
ele_partner = img_partner->ele_info->ele;
|
||||||
|
- if (full_length(img_partner, CUTOFF2)) ele_partner->flimg_no --;
|
||||||
|
+ if (full_length(img_partner, CUTOFF2)){
|
||||||
|
+ ele_partner->flimg_no --;
|
||||||
|
+ }
|
||||||
|
tbd_tmp = cur_ele->TBD;
|
||||||
|
while (tbd_tmp != NULL) {
|
||||||
|
if (tbd_tmp->bd > cur_img_data->to_image->frag.lb || !tbd_tmp->next) {
|
||||||
|
if (tbd_tmp->bd > cur_img_data->to_image->frag.lb && tbd_tmp->bd < cur_img_data->to_image->frag.rb) {
|
||||||
|
if (tbd_tmp->bd - cur_img_data->to_image->frag.lb <= TOO_SHORT) {
|
||||||
|
- cur_img_data->to_image->to_msp->score = (long) (cur_img_data->to_image->frag.rb-tbd_tmp->bd+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
|
||||||
|
+ cur_img_data->to_image->to_msp->score = (int32_t) (cur_img_data->to_image->frag.rb-tbd_tmp->bd+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
|
||||||
|
if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.lb += tbd_tmp->bd - cur_img_data->to_image->frag.lb;
|
||||||
|
else img_partner->frag.rb -= tbd_tmp->bd - cur_img_data->to_image->frag.lb;
|
||||||
|
cur_img_data->to_image->frag.lb = tbd_tmp->bd;
|
||||||
|
} else if (tbd_tmp->bd - cur_img_data->to_image->frag.rb >= -TOO_SHORT) {
|
||||||
|
- cur_img_data->to_image->to_msp->score = (long) (tbd_tmp->bd-cur_img_data->to_image->frag.lb+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
|
||||||
|
+ cur_img_data->to_image->to_msp->score = (int32_t) (tbd_tmp->bd-cur_img_data->to_image->frag.lb+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
|
||||||
|
if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.rb -= cur_img_data->to_image->frag.rb - tbd_tmp->bd;
|
||||||
|
else img_partner->frag.lb += cur_img_data->to_image->frag.rb - tbd_tmp->bd;
|
||||||
|
cur_img_data->to_image->frag.rb = tbd_tmp->bd;
|
||||||
|
@@ -1375,8 +1415,11 @@
|
||||||
|
target_img = &msp_tmp->sbjct;
|
||||||
|
target_partner = &msp_tmp->query;
|
||||||
|
}
|
||||||
|
- msp_tmp->score = (long) (tbd_tmp->bd-target_img->frag.lb+1.)/(target_img->frag.rb-target_img->frag.lb+1.)*msp_tmp->score;
|
||||||
|
+ msp_tmp->score = (int32_t) (tbd_tmp->bd-target_img->frag.lb+1.)/(target_img->frag.rb-target_img->frag.lb+1.)*msp_tmp->score;
|
||||||
|
if (msp_tmp->direction == 1) {
|
||||||
|
+ // RMH: When tracking down the divide by zero problem I ended up signaling this
|
||||||
|
+ // spot in the code as the likely place where things went initially wrong.
|
||||||
|
+ // Explore further.
|
||||||
|
target_partner->frag.rb -= target_img->frag.rb - tbd_tmp->bd;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
@@ -1715,7 +1758,7 @@
|
||||||
|
ELE_DATA_t *ele_data_tmp;
|
||||||
|
IMG_DATA_t *scovs;
|
||||||
|
|
||||||
|
- long max_score=0;
|
||||||
|
+ int32_t max_score=0;
|
||||||
|
short dir;
|
||||||
|
|
||||||
|
/* sort unprocessed images according to their partner element, and then their left bounds */
|
||||||
|
@@ -1862,7 +1905,10 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-
|
||||||
|
+/* NOTE: Due to the difference in computational precesion between 32bit
|
||||||
|
+ * and 64 bit processors the following function may return differing
|
||||||
|
+ * results.
|
||||||
|
+ */
|
||||||
|
int full_length(IMAGE_t *i, float cutoff) {
|
||||||
|
if (!i->ele_info->ele) {
|
||||||
|
err_no ++;
|
||||||
|
@@ -1879,7 +1925,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-void add_CP(CP_t **CP_ptr, long cp, ELE_INFO_t *cont) {
|
||||||
|
+void add_CP(CP_t **CP_ptr, int32_t cp, ELE_INFO_t *cont) {
|
||||||
|
CP_t *new = (CP_t *) malloc(sizeof(CP_t));
|
||||||
|
new->cp = cp;
|
||||||
|
new->contributor = cont;
|
||||||
|
@@ -1889,7 +1935,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-void add_edge(ELE_INFO_t *ele1_info, ELE_INFO_t *ele2_info, char type, long score, short dir) {
|
||||||
|
+void add_edge(ELE_INFO_t *ele1_info, ELE_INFO_t *ele2_info, char type, int32_t score, short dir) {
|
||||||
|
EDGE_t *new = EDGE_malloc();
|
||||||
|
int ct;
|
||||||
|
|
||||||
|
@@ -2078,7 +2124,7 @@
|
||||||
|
*/
|
||||||
|
|
||||||
|
#if 0
|
||||||
|
-int find_prim(IMG_NODE_t *nd, float cutoff, long score, long hist, short which, long *sc, short *d) {
|
||||||
|
+int find_prim(IMG_NODE_t *nd, float cutoff, int32_t score, int32_t hist, short which, int32_t *sc, short *d) {
|
||||||
|
IMG_NODE_t *nex_node;
|
||||||
|
int sum = 0;
|
||||||
|
short level, further = 0;
|
||||||
|
@@ -2143,9 +2189,9 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-int find_prim(IMG_NODE_t *nd, float cutoff, long end1, long end2, long efl1, long efl2, long al1, long al2, long score, int *pmarkp, long *sc, short *d) {
|
||||||
|
+int find_prim(IMG_NODE_t *nd, float cutoff, int32_t end1, int32_t end2, int32_t efl1, int32_t efl2, int32_t al1, int32_t al2, int32_t score, int *pmarkp, int32_t *sc, short *d) {
|
||||||
|
int sum = 0, mark=0;
|
||||||
|
- long skip1, skip2, len1, len2;
|
||||||
|
+ int32_t skip1, skip2, len1, len2;
|
||||||
|
IMAGE_t *ipt;
|
||||||
|
|
||||||
|
if (nd->sib) sum += find_prim(nd->sib, cutoff, end1, end2, efl1, efl2, al1, al2, score, pmarkp, sc, d);
|
||||||
|
@@ -2169,7 +2215,7 @@
|
||||||
|
efl2 += len2;
|
||||||
|
al1 += len1;
|
||||||
|
al2 += len2;
|
||||||
|
- score += ((long) nd->to_image->to_msp->iden)*(len1+len2)/2;
|
||||||
|
+ score += ((int32_t) nd->to_image->to_msp->iden)*(len1+len2)/2;
|
||||||
|
|
||||||
|
if (nd->children) {
|
||||||
|
end1 = nd->to_image->frag.rb;
|
||||||
|
@@ -2188,6 +2234,16 @@
|
||||||
|
if ( (1.0*al1/efl1 > cutoff || 1.0*al2/efl2 > cutoff) && (efl1-al1 < 30 || efl2-al2 < 30) ) {
|
||||||
|
sum = 1;
|
||||||
|
mark = 1;
|
||||||
|
+ if ( (al1+al2) == 0 )
|
||||||
|
+ {
|
||||||
|
+ // RMH: A divide by zero error has occured a few times at this point.
|
||||||
|
+ // I looked extensively through the code and cannot determine what
|
||||||
|
+ // is causing this -- although I have a reliable test case to
|
||||||
|
+ // explore this further. For now this is the only workaround.
|
||||||
|
+ // If al1 & al2 are zero then simply set them to 1.
|
||||||
|
+ printf("eleredef warning: Divide by zero averted -- setting al1 to 1.\n");
|
||||||
|
+ al1 = 1;
|
||||||
|
+ }
|
||||||
|
score = score*2/(al1+al2);
|
||||||
|
if (score > *sc) {
|
||||||
|
*sc = score;
|
||||||
|
diff -ruN RECON1.05/src/Makefile RECON-1.08/src/Makefile
|
||||||
|
--- RECON1.05/src/Makefile 2002-01-10 15:48:02.000000000 -0600
|
||||||
|
+++ RECON-1.08/src/Makefile 2014-02-05 16:05:18.000000000 -0600
|
||||||
|
@@ -1,9 +1,7 @@
|
||||||
|
# Makefile for ReCon
|
||||||
|
#
|
||||||
|
#
|
||||||
|
-
|
||||||
|
-VERSION = 1.0
|
||||||
|
-VDATE = JUL 2001
|
||||||
|
+VERSION = 1.08
|
||||||
|
|
||||||
|
## where you want things installed
|
||||||
|
BINDIR = ../bin
|
||||||
|
@@ -13,8 +11,8 @@
|
||||||
|
#SRCDIR = .
|
||||||
|
|
||||||
|
## your compiler
|
||||||
|
-CC = gcc
|
||||||
|
#CC = cc # for SGI Origin200 compiler#
|
||||||
|
+CC = gcc
|
||||||
|
|
||||||
|
## any special compiler flags you want
|
||||||
|
# -pedantic clashes with -DMEMDEBUG??
|
||||||
|
@@ -121,7 +119,5 @@
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
-
|
||||||
|
-
|
||||||
|
|
||||||
|
|
||||||
|
diff -ruN RECON1.05/src/msps.h RECON-1.08/src/msps.h
|
||||||
|
--- RECON1.05/src/msps.h 2002-01-10 15:19:10.000000000 -0600
|
||||||
|
+++ RECON-1.08/src/msps.h 2014-02-05 16:05:18.000000000 -0600
|
||||||
|
@@ -3,14 +3,13 @@
|
||||||
|
#include "bolts.h"
|
||||||
|
#include "seqlist.h"
|
||||||
|
|
||||||
|
-
|
||||||
|
/* A collection of structures and functions to handle MSPs */
|
||||||
|
|
||||||
|
/* BASIC structures */
|
||||||
|
|
||||||
|
typedef struct frag {
|
||||||
|
char *seq_name;
|
||||||
|
- long lb, rb;
|
||||||
|
+ int32_t lb, rb;
|
||||||
|
/* char lst, rst; type of ends, can be used to mark physical ends */
|
||||||
|
} FRAG_t;
|
||||||
|
|
||||||
|
@@ -44,7 +43,7 @@
|
||||||
|
typedef struct msp {
|
||||||
|
/*struct msp_list *hanger;*/
|
||||||
|
char stat; /* 'p', 's' */
|
||||||
|
- long score;
|
||||||
|
+ int32_t score;
|
||||||
|
float iden;
|
||||||
|
int direction;
|
||||||
|
IMAGE_t query, sbjct;
|
||||||
|
@@ -110,7 +109,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
int scan_msp(MSP_t *m, char *line) {
|
||||||
|
- long bd_tmp;
|
||||||
|
+ int32_t bd_tmp;
|
||||||
|
char qname[NAME_LEN], sname[NAME_LEN];
|
||||||
|
int pos;
|
||||||
|
|
||||||
|
@@ -153,7 +152,7 @@
|
||||||
|
/* archaine */
|
||||||
|
#if 0
|
||||||
|
int merge_msp(MSP_t *m1, MSP_t *m2) { /* merge two MSPs into the first one */
|
||||||
|
- long l1, l2;
|
||||||
|
+ int32_t l1, l2;
|
||||||
|
|
||||||
|
/* no need for changing direction */
|
||||||
|
/* iden */
|
||||||
|
@@ -195,7 +194,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
int sing_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) {
|
||||||
|
- long l1, l2, l, lb, rb;
|
||||||
|
+ int32_t l1, l2, l, lb, rb;
|
||||||
|
if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) {
|
||||||
|
l1 = f1->rb - f1->lb;
|
||||||
|
l2 = f2->rb - f2->lb;
|
||||||
|
@@ -211,7 +210,7 @@
|
||||||
|
|
||||||
|
|
||||||
|
int doub_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) {
|
||||||
|
- long l1, l2, l, lb, rb;
|
||||||
|
+ int32_t l1, l2, l, lb, rb;
|
||||||
|
if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) {
|
||||||
|
l1 = f1->rb - f1->lb;
|
||||||
|
l2 = f2->rb - f2->lb;
|
||||||
|
diff -ruN RECON1.05/src/seqlist.h RECON-1.08/src/seqlist.h
|
||||||
|
--- RECON1.05/src/seqlist.h 2002-01-10 15:19:10.000000000 -0600
|
||||||
|
+++ RECON-1.08/src/seqlist.h 2014-02-05 16:05:18.000000000 -0600
|
||||||
|
@@ -1,5 +1,6 @@
|
||||||
|
|
||||||
|
#include "bolts.h"
|
||||||
|
+#include "string.h"
|
||||||
|
|
||||||
|
#ifndef _seqlist_h
|
||||||
|
#define _seqlist_h
|
||||||
Loading…
Reference in a new issue