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Merge pull request #5 from gtamazian/master
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Fixes for compilation under OS X
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@siepellab
siepellab committed Jun 2, 2016
2 parents a1262f2 + a745778 commit 515708b
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Showing 4 changed files with 41 additions and 34 deletions.
7 changes: 7 additions & 0 deletions .gitignore
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@@ -0,0 +1,7 @@
*.a
*.o
*.help

bin/
doc/man/

2 changes: 1 addition & 1 deletion include/external_libs.h
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Expand Up @@ -33,7 +33,7 @@
#else

#ifdef VECLIB
#include <vecLib/clapack.h>
#include <Accelerate/Accelerate.h>
#define LAPACK_INT __CLPK_integer
#define LAPACK_DOUBLE __CLPK_doublereal
#else
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2 changes: 1 addition & 1 deletion src/make-include.mk
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Expand Up @@ -133,7 +133,7 @@ endif
# vecLib
ifdef VECLIB
CFLAGS += -DVECLIB
LIBS = -lphast -framework vecLib -lc -lm
LIBS = -lphast -framework Accelerate -lc -lm

# CLAPACK
else
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64 changes: 32 additions & 32 deletions src/util/clean_genes.c
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Expand Up @@ -34,16 +34,16 @@
typedef enum {OKAY, BAD_REF, BAD_REF_START, BAD_REF_STOP, BAD_REF_5_SPLICE,
BAD_REF_3_SPLICE, BAD_REF_ORF, BAD_REF_INDEL_STRICT_FAIL,
NO_ALN, BAD_START, BAD_STOP, BAD_5_SPLICE, BAD_3_SPLICE,
BAD_5_SPLICE_UTR, BAD_3_SPLICE_UTR, NONSENSE, FSHIFT,
BAD_INTRON, TOO_MANY_Ns, WARN_FSHIFT, WARN_Ns, NTYPES}
BAD_5_SPLICE_UTR, BAD_3_SPLICE_UTR, NONSENSE, FRAMESHIFT,
BAD_INTRON, TOO_MANY_Ns, WARN_FRAMESHIFT, WARN_Ns, NTYPES}
status_type; /* NTYPES marks the total number */

/* possible gap types for cds exon -- frame-shift gaps (FSHIFT_BAD),
no apparent frame shift (FSHIFT_OK), all gaps multiple of 3 in len
/* possible gap types for cds exon -- frame-shift gaps (FRAMESHIFT_BAD),
no apparent frame shift (FRAMESHIFT_OK), all gaps multiple of 3 in len
(CLN_GAPS), gaps mult. of 3 and nonoverlapping (NOVRLP_CLN_GAPS),
and no gaps present (NGAPS). Defined in order of least to most
stringent criterion (ordering gets used) */
typedef enum {FSHIFT_BAD, FSHIFT_OK, CLN_GAPS,
typedef enum {FRAMESHIFT_BAD, FRAMESHIFT_OK, CLN_GAPS,
NOVRLP_CLN_GAPS, NGAPS, NGAP_TYPES}
cds_gap_type; /* NGAP_TYPES marks the total number */

Expand Down Expand Up @@ -102,7 +102,7 @@ typedef struct Problem {
status_type status;
int start;
int end;
cds_gap_type cds_gap; /* if status if FSHIFT */
cds_gap_type cds_gap; /* if status if FRAMESHIFT */
} Problem;

/* create a new problem. feat can be null for whole gene.
Expand Down Expand Up @@ -311,7 +311,7 @@ int gap_compare(const void *ptr1, const void* ptr2) {
return g1->start - g2->start;
}
/* scans a cds for gaps. Returns CLN_GAPS, NOVRLP_CLN_GAPS, NO_GAPS,
or FSHIFT_BAD; doesn't try to check for compensatory indels, which
or FRAMESHIFT_BAD; doesn't try to check for compensatory indels, which
is more complicated (this is left for the special-purpose function
below) */
int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
Expand All @@ -322,7 +322,7 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
cds_gap_type retval = NGAPS;
List *gaps = lst_new_ptr(10);

for (j = 0; retval != FSHIFT_BAD && j < msa->nseqs; j++) {
for (j = 0; retval != FRAMESHIFT_BAD && j < msa->nseqs; j++) {
for (i = msa_start; i <= msa_end; i++) {
if (ss_get_char_pos(msa, i, j, 0) == GAP_CHAR) {
int gap_start, gap_end;
Expand All @@ -336,9 +336,9 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
gap_end--; /* inclusive */

if ((gap_end - gap_start + 1) % 3 != 0) {
retval = FSHIFT_BAD;
*problem = problem_new(feat, FSHIFT, gap_start, gap_end);
(*problem)->cds_gap = FSHIFT_BAD;
retval = FRAMESHIFT_BAD;
*problem = problem_new(feat, FRAMESHIFT, gap_start, gap_end);
(*problem)->cds_gap = FRAMESHIFT_BAD;
break;
}

Expand Down Expand Up @@ -449,18 +449,18 @@ int is_fshift_okay(GFF_Feature *feat, MSA *msa) {
"clean" gaps (all multiples of 3 in length; CLEAN_GAPS)
non-overlapping clean gaps (NOVRLP_CLN_GAPS), "okay" gaps (only
temporary frame shifts, corrected by compensatory indels;
FSHIFT_OK), or real frame-shift gaps (FSHIFT_BAD) */
FRAMESHIFT_OK), or real frame-shift gaps (FRAMESHIFT_BAD) */
cds_gap_type get_cds_gap_type(GFF_Feature *feat, MSA *msa, List *problems) {
Problem *problem = NULL;
cds_gap_type retval = scan_for_gaps(feat, msa, &problem);

if (retval == FSHIFT_BAD && is_fshift_okay(feat, msa)) {
retval = FSHIFT_OK;
if (retval == FRAMESHIFT_BAD && is_fshift_okay(feat, msa)) {
retval = FRAMESHIFT_OK;
/* most of the time the call to
is_fshift_okay won't be
necessary */
problem->status = WARN_FSHIFT;
problem->cds_gap = FSHIFT_OK;
problem->status = WARN_FRAMESHIFT;
problem->cds_gap = FRAMESHIFT_OK;
}
if (problem != NULL) {
lst_push_ptr(problems, problem);
Expand Down Expand Up @@ -669,9 +669,9 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,
case NONSENSE:
reason = "Nonsense mutation";
break;
case FSHIFT:
case FRAMESHIFT:
{
if (problem->cds_gap == FSHIFT_OK)
if (problem->cds_gap == FRAMESHIFT_OK)
reason = "Frame-shift gap [gaps not clean]";
else if (problem->cds_gap == CLN_GAPS)
reason = "Frame-shift gap [gaps clean but overlapping/near boundary]";
Expand All @@ -689,7 +689,7 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,
reason = "Too many Ns";
print_alignment = FALSE;
break;
case WARN_FSHIFT:
case WARN_FRAMESHIFT:
reason = "Frame shift gap (with compensatory gap)";
break;
case WARN_Ns:
Expand Down Expand Up @@ -741,13 +741,13 @@ char *status_type_str(status_type status) {
return "bad_3_splice_utr";
case NONSENSE:
return "nonsense";
case FSHIFT:
case FRAMESHIFT:
return "frameshift";
case BAD_INTRON:
return "bad_intron";
case TOO_MANY_Ns:
return "too_many_Ns";
case WARN_FSHIFT:
case WARN_FRAMESHIFT:
return "warning_fshift";
case WARN_Ns:
return "warning_Ns";
Expand Down Expand Up @@ -980,7 +980,7 @@ int main(int argc, char *argv[]) {
*discards=NULL, *intron_splice = lst_new_ptr(10);
char *rseq_fname = NULL;
FILE *logf = NULL, *mlogf = NULL, *statsf = NULL, *discardf = NULL;
cds_gap_type fshift_mode = FSHIFT_BAD;
cds_gap_type fshift_mode = FRAMESHIFT_BAD;
char *groupby = "transcript_id";
msa_coord_map *map;
int *countNs, *countCDSs;
Expand Down Expand Up @@ -1029,11 +1029,11 @@ int main(int argc, char *argv[]) {
break;
case 'f':
check_alignment = 1;
fshift_mode = FSHIFT_OK;
fshift_mode = FRAMESHIFT_OK;
break;
case 'c':
check_alignment = check_start = check_stop = check_splice = check_nonsense = 1;
if (fshift_mode < FSHIFT_OK) fshift_mode = FSHIFT_OK;
if (fshift_mode < FRAMESHIFT_OK) fshift_mode = FRAMESHIFT_OK;
break;
case 'N':
Nfrac = get_arg_dbl_bounds(optarg, 0, 1);
Expand Down Expand Up @@ -1166,7 +1166,7 @@ int main(int argc, char *argv[]) {
List *gfeatures = group->features;
GFF_Feature *feat;
status_type status = OKAY;
cds_gap_type gt = FSHIFT_BAD;
cds_gap_type gt = FRAMESHIFT_BAD;
problems_clear(problems);

/* make sure have frame info for CDSs */
Expand Down Expand Up @@ -1295,9 +1295,9 @@ int main(int argc, char *argv[]) {

else if (str_equals_charstr(feat->feature, GFF_CDS_TYPE)) {

if (fshift_mode > FSHIFT_BAD
if (fshift_mode > FRAMESHIFT_BAD
&& (gt = get_cds_gap_type(feat, msa, problems)) < fshift_mode) {
if (status == OKAY || status == NONSENSE) status = FSHIFT;
if (status == OKAY || status == NONSENSE) status = FRAMESHIFT;
}

if (check_nonsense && !is_nonsense_clean(feat, msa, problems)) {
Expand Down Expand Up @@ -1336,8 +1336,8 @@ int main(int argc, char *argv[]) {
for (j = 0; j < lst_size(problems); j++) {
struct Problem *problem = lst_get_ptr(problems, j);
status_type ftype = problem->status;
if ((ftype == FSHIFT || ftype == NONSENSE) &&
status != FSHIFT && status != NONSENSE)
if ((ftype == FRAMESHIFT || ftype == NONSENSE) &&
status != FRAMESHIFT && status != NONSENSE)
continue; /* don't count secondary frame shifts
and nonsense mutations */

Expand All @@ -1350,7 +1350,7 @@ int main(int argc, char *argv[]) {

/* also keep track of the total number of "conserved exons", and
the number having each kind of gap */
if ((status == OKAY || (status == FSHIFT && gt >= FSHIFT_OK))) {
if ((status == OKAY || (status == FRAMESHIFT && gt >= FRAMESHIFT_OK))) {
nconserved_exons++;
nce_gap_type[gt]++; /* number of conserved exons having
given type of gaps */
Expand Down Expand Up @@ -1429,10 +1429,10 @@ int main(int argc, char *argv[]) {
nconsid[BAD_5_SPLICE], nfail[BAD_3_SPLICE], nconsid[BAD_3_SPLICE],
nfail[BAD_5_SPLICE_UTR], nconsid[BAD_5_SPLICE_UTR],
nfail[BAD_3_SPLICE_UTR], nconsid[BAD_3_SPLICE_UTR],
nfail[BAD_INTRON], nfail[NONSENSE], nfail[FSHIFT],
nfail[BAD_INTRON], nfail[NONSENSE], nfail[FRAMESHIFT],
nfail[TOO_MANY_Ns], nconserved_exons, nce_gap_type[NGAPS],
nce_gap_type[NOVRLP_CLN_GAPS], nce_gap_type[CLN_GAPS],
nce_gap_type[FSHIFT_OK]);
nce_gap_type[FRAMESHIFT_OK]);
fprintf(statsf, "%s", STATS_DESCRIPTION);
}

Expand Down

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