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recon: new package at 1.08 (#11408)

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* 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 2019-05-15 15:55:10 -05:00 committed by Levi Baber
parent 80d7573df8
commit 62fa813678
2 changed files with 635 additions and 0 deletions
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52
var/spack/repos/builtin/packages/recon/package.py Normal file
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@ -0,0 +1,52 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
from os import symlink
class Recon(MakefilePackage):
"""RECON: a package for automated de novo identification of repeat families
from genomic sequences."""
homepage = "http://eddylab.org/software/recon/"
url = "http://eddylab.org/software/recon/RECON1.05.tar.gz"
version('1.05', sha256='4d4f76f439bcffd50380cffc41a80dc15fa4a80f38a04234e24da893ed7c025a')
variant('repeatmasker', default=False,
description='Use RepeatMasker developer patches (1.08)')
patch('repeatmasker_recon.patch', when='+repeatmasker')
build_directory = 'src'
depends_on('perl', type='run')
@property
def install_targets(self):
return [
'install',
'BINDIR=%s' % self.prefix.bin
]
# edit the recon.pl script with the prefix as mentioned in the README
def edit(self, spec, prefix):
filter_file('$path = ""', '$path = "%s"' % prefix.bin,
'scripts/recon.pl', string=True)
# recon's makefile is very basic -- the target directory must
# already exist to properly install
@run_before('install')
def prepare_bin(self):
mkdirp(prefix.bin)
# finally, install the scripts dir as well
# and link the recon command into bin.
@run_after('install')
def finalize(self):
install_tree('scripts', prefix.scripts)
symlink(join_path(prefix.scripts, 'recon.pl'),
join_path(prefix.bin, 'recon'))

583
var/spack/repos/builtin/packages/recon/repeatmasker_recon.patch Normal file
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@ -0,0 +1,583 @@
diff -ruN RECON1.05/00README RECON-1.08/00README
--- RECON1.05/00README 2002-04-08 14:31:59.000000000 -0500
+++ RECON-1.08/00README 2014-02-05 16:05:18.000000000 -0600
@@ -1,6 +1,7 @@
RECON -- finding repeat families from biological sequences
-Version 1.03 (Mar 2002)
+Version 1.08 (Jan 2014)
Copyright (C) 2001 Washington University School of Medicine
+Copyright (C) 2011-2014 Institute for Systems Biology
------------------------------------------------------------------
@@ -28,8 +29,26 @@
What's new?
+RECON1.08: Wed Feb 5 14:04:25 PST 2014 - Robert Hubley ISB
+ - New checks in eleredef.c for failed memory allocation/file operations.
+ - A buffer overrun bug fix provided by Stephen Ficklin in eledef.c.
+
+RECON1.07: Wed Jun 8 10:00:55 PDT 2011 - Robert Hubley ISB
+ - Another problem with the eleredef program has appeared a couple
+ of times. A divide by zero error in one of Zhirong's routines.
+ I have applied a workaround to the divide by zero but not a fix
+ to the real problem. The program will now warn the user if
+ the workaround was exercised during a run.
+
+RECON1.06: Tue May 20 15:19:30 PDT 2008 - Robert Hubley ISB
+ - 64 bit compiler fixes: Previous versions of RECON used the "long"
+ data type under the assumption that was 32bits. This caused the
+ program to crash or lock up during analysis.
+
Bug fix for RECON1.02 in the eleredef program.
+
+
Programs and input
The RECON algorithm defines repeat families on the basis of pairwise
@@ -50,7 +69,6 @@
multiple times and concatenate the result into one MSP file.
-
The recon script drives the running of the package. The command
line format is as follows:
diff -ruN RECON1.05/src/bolts.h RECON-1.08/src/bolts.h
--- RECON1.05/src/bolts.h 2002-01-10 15:19:09.000000000 -0600
+++ RECON-1.08/src/bolts.h 2014-02-05 16:05:18.000000000 -0600
@@ -10,5 +10,5 @@
-long seq_no;
+int32_t seq_no;
char **seq_names;
diff -ruN RECON1.05/src/edgeredef.c RECON-1.08/src/edgeredef.c
--- RECON1.05/src/edgeredef.c 2002-07-19 10:42:03.000000000 -0500
+++ RECON-1.08/src/edgeredef.c 2014-02-05 16:05:18.000000000 -0600
@@ -58,6 +58,10 @@
}
log_file = fopen("tmp2/log", "w");
+ if (!log_file) {
+ printf("Can not open log_file. Exiting\n");
+ exit(1);
+ }
while (fgets(line, 15, ele_no)) {
ele_ct = atoi(line);
@@ -191,7 +195,7 @@
} else {
ele_info->stat = 'y';
ele_cleanup(&ele_info->ele);
- command = (char *) malloc(30*sizeof(char));
+ command = (char *) malloc(80*sizeof(char));
sprintf(command, "cp tmp/e%d tmp2/.", ele_info->index);
system(command);
free(command);
diff -ruN RECON1.05/src/eledef.c RECON-1.08/src/eledef.c
--- RECON1.05/src/eledef.c 2002-01-10 15:19:10.000000000 -0600
+++ RECON-1.08/src/eledef.c 2014-02-05 16:05:18.000000000 -0600
@@ -385,7 +385,7 @@
void img_charge(IPROT_t **shadow, int ct, FILE *input) {
int i=0, pos=0;
- char line[100];
+ char line[151];
int scan_flag;
MSP_t msp;
diff -ruN RECON1.05/src/ele.h RECON-1.08/src/ele.h
--- RECON1.05/src/ele.h 2002-01-10 15:19:09.000000000 -0600
+++ RECON-1.08/src/ele.h 2014-02-05 16:05:18.000000000 -0600
@@ -1,7 +1,6 @@
#include "msps.h"
-
#define SIZE_LIMIT 500
#define TANDEM 5
@@ -9,13 +8,13 @@
typedef struct cp_list {
- long cp;
+ int32_t cp;
struct ele_info *contributor;
struct cp_list *next;
} CP_t;
typedef struct bd_list {
- long bd;
+ int32_t bd;
int support;
struct bd_list *next;
} BD_t;
@@ -24,7 +23,7 @@
int index;
char type; /* 'p', 's', 'c' */
int direction; /* for clustering elements in consistent directions */
- long score; /* for edge_filt, to solve the PPS problem */
+ int32_t score; /* for edge_filt, to solve the PPS problem */
struct ele_info *ele1_info, *ele2_info;
} EDGE_t;
@@ -67,6 +66,7 @@
struct ele_list *next;
} ELE_DATA_t;
+
typedef struct family {
int index;
char name[10];
@@ -139,21 +139,45 @@
void frag_data_free(FRAG_DATA_t **);
void frag_data_cleanup(FRAG_DATA_t **);
-
+void print_ele_info(ELE_INFO_t *rt);
+void print_ele_data(ELE_DATA_t *rt);
/*MSP_DATA_t *all_msps=NULL;
EDGE_t *efav=NULL;*/
ELE_INFO_t **all_ele;
int ele_ct, ele_array_size, fam_ct;
int clan_size, clan_core_size;
-long msp_in_mem, msp_left, msp_ct, msp_index;
-long edge_index, edge_in_mem, edge_left, edge_ct;
-long files_read, clan_ct, err_no;
+int32_t msp_in_mem, msp_left, msp_ct, msp_index;
+int32_t edge_index, edge_in_mem, edge_left, edge_ct;
+int32_t files_read, clan_ct, err_no;
ELE_INFO_t *ele_info_data, *ele_info_tail;
FAM_DATA_t *FAMs;
FILE *err, *new_msps, *eles, *unproc, *combo, *obs, *fams, *log_file;
+/***************
+ * DEBUG *
+ ***************/
+
+void print_ele_data(ELE_DATA_t *rt) {
+ if (!rt) return;
+ print_ele_info( rt->ele_info );
+ if (rt->next)
+ print_ele_data(rt->next);
+}
+
+void print_ele_info(ELE_INFO_t *rt) {
+ if (!rt) return;
+ printf("ele: index=%d, stat=%c, file_update=%d", rt->index, rt->stat,
+ rt->file_updated );
+ if ( rt->to_family )
+ printf(" family_index=%d,", rt->to_family->index );
+ if ( rt->ele )
+ printf(" ele_index=%d", rt->ele->index );
+ else
+ printf(" ele=NULL");
+ printf("\n");
+}
@@ -1341,7 +1365,7 @@
-
+/* Unused */
void msp_data_free(MSP_DATA_t **md) {
MSP_DATA_t *cur, *next;
diff -ruN RECON1.05/src/eleredef.c RECON-1.08/src/eleredef.c
--- RECON1.05/src/eleredef.c 2002-03-22 14:01:54.000000000 -0600
+++ RECON-1.08/src/eleredef.c 2014-02-05 16:05:18.000000000 -0600
@@ -51,7 +51,7 @@
BD_t *CP_cluster(CP_t *);
void CP_sort(CP_t **);
void BD_sort(BD_t **);
-int span(ELEMENT_t *, long);
+int span(ELEMENT_t *, int32_t);
void TBD_merge(ELEMENT_t *);
void dissect(ELE_INFO_t *);
@@ -67,16 +67,16 @@
void edges_and_cps(ELE_INFO_t *, IMAGE_t **);
int full_length(IMAGE_t *, float);
-void add_CP(CP_t **, long, ELE_INFO_t *);
-void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, long, short);
+void add_CP(CP_t **, int32_t, ELE_INFO_t *);
+void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, int32_t, short);
void adjust_edge_tree(ELE_INFO_t *);
int charge_edge_array(EDGE_t **, EDGE_TREE_t *, int);
int consis_tree_build(IMG_NODE_t *, IMAGE_t *, int);
int consis(IMAGE_t *, IMAGE_t *, float);
IMG_NODE_t **node_entry(IMG_NODE_t **);
void consis_tree_free(IMG_NODE_t *);
-/*int find_prim(struct img_node *, float, long, long, short, long *, short *);*/
-int find_prim(IMG_NODE_t *, float, long, long, long, long, long, long, long, int *, long *, short *);
+/*int find_prim(struct img_node *, float, int32_t, int32_t, short, int32_t *, short *);*/
+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 *);
void combo_output(ELE_INFO_t *);
void obs_output(ELE_INFO_t *);
@@ -90,9 +90,6 @@
-
-
-
int main (int argc, char *argv[]) {
ELE_INFO_t *cur_ele_info;
int i, ele_march, ei, rounds=0, start;
@@ -125,7 +122,6 @@
printf("Can not open naive_ele_no. Exiting\n");
exit(1);
}
-
msp_no = fopen("summary/redef_msp_no", "r");
if (!msp_no) msp_no = fopen("summary/ori_msp_no", "r");
if (!msp_no) {
@@ -133,15 +129,46 @@
exit(1);
}
+ // May or may not exist. All uses of edge_no first check for
+ // its existence.
edge_no = fopen("summary/naive_edge_no", "r");
+
+ // May or may not exist. All uses are checked.
size_list = fopen("tmp/size_list", "r");
+
+ // May or may not exist. All uses are checked.
new_stat = fopen("tmp2/redef_stat", "r");
new_msps = fopen("summary/new_msps", "a");
+ if ( !new_msps )
+ {
+ printf("Can not open summary/new_msps for writing! Exiting\n");
+ exit(1);
+ }
unproc = fopen("summary/unproc", "a");
+ if ( !unproc )
+ {
+ printf("Can not open summary/unproc for writing! Exiting\n");
+ exit(1);
+ }
combo = fopen("summary/combo", "a");
+ if ( !combo )
+ {
+ printf("Can not open summary/combo for writing! Exiting\n");
+ exit(1);
+ }
obs = fopen("summary/obsolete", "a");
+ if ( !obs )
+ {
+ printf("Can not open summary/obsolete for writing! Exiting\n");
+ exit(1);
+ }
log_file = fopen("tmp2/log", "a");
+ if ( !log_file )
+ {
+ printf("Can not open tmp2/log for writing! Exiting\n");
+ exit(1);
+ }
while (fgets(line, 15, ele_no)) {
ele_ct = atoi(line);
@@ -170,7 +197,7 @@
if (size_list && !new_stat) outthrow_big_tandems(size_list);
fclose(unproc);
- /* 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