[med-svn] [Git][med-team/gmap][upstream] New upstream version 2021-02-12+ds
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Feb 19 16:07:28 GMT 2021
Michael R. Crusoe pushed to branch upstream at Debian Med / gmap
Commits:
0ba0084d by Michael R. Crusoe at 2021-02-19T16:31:52+01:00
New upstream version 2021-02-12+ds
- - - - -
11 changed files:
- ChangeLog
- VERSION
- src/filestring.c
- src/genome128_hr.c
- src/gmap.c
- src/gsnap.c
- src/outbuffer.c
- src/output.c
- src/resulthr.c
- src/stage3hr.c
- src/stage3hr.h
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,36 @@
+2021-02-14 twu
+
+ * index.html: Updated for latest version
+
+ * outbuffer.c: Added comment
+
+2021-02-13 twu
+
+ * outbuffer.c: Calling setvbuf before printing file headers
+
+ * gmap.c, gsnap.c: Added comments
+
+ * output.c: Fixed code for deciding on failed input for single-end reads
+
+ * VERSION, index.html: Updated version number
+
+ * output.c: Using the results of Stage3pair_print_end to determine whether a
+ sequence failed to print
+
+ * stage3hr.c, stage3hr.h: Stage3pair_print_end now returns whether it
+ printed an alignment
+
+ * gsnap.c: Formatting change
+
+ * genome128_hr.c: Removed extraneous semicolon at end of macro
+
+ * outbuffer.c: Checking for a NULL string from Filestring_T before pushing
+ onto the failedinput Filestring_T
+
+ * resulthr.c: Fixed a memory leak
+
+ * filestring.c: Removed faulty assertion
+
2020-12-16 twu
* outbuffer.c: Added option for using write instead of fwrite
=====================================
VERSION
=====================================
@@ -1 +1 @@
-2020-12-17
\ No newline at end of file
+2021-02-12
\ No newline at end of file
=====================================
src/filestring.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: filestring.c 223773 2020-12-14 19:15:02Z twu $";
+static char rcsid[] = "$Id: filestring.c 223803 2021-02-13 17:17:15Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -63,7 +63,9 @@ Filestring_split_output (T this) {
char *
Filestring_string (T this) {
- assert(this->string != NULL); /* Because we assume that Filestring_stringify has been called */
+ /* Because we assume that Filestring_stringify has been called */
+ /* But could be NULL */
+ /* assert(this->string != NULL); */
return this->string;
}
=====================================
src/genome128_hr.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome128_hr.c 223551 2020-11-15 19:43:52Z twu $";
+static char rcsid[] = "$Id: genome128_hr.c 223806 2021-02-13 18:45:39Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -4186,7 +4186,7 @@ clear_lowbit_128 (__m128i _diff, int relpos) {
#define clear_highbit_32(diff,relpos) (diff ^ (HIGH_BIT >> relpos))
/* Slower: clear_lowbit(diff,relpos) diff -= (1 << relpos) */
-#define clear_lowbit_32(diff,relpos) (diff & (diff - 1));
+#define clear_lowbit_32(diff,relpos) (diff & (diff - 1))
#if !defined(HAVE_SSE4_2)
=====================================
src/gmap.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmap.c 223772 2020-12-14 19:14:33Z twu $";
+static char rcsid[] = "$Id: gmap.c 223812 2021-02-14 00:01:36Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -4863,6 +4863,7 @@ worker_thread (void *data) {
Stopwatch_T worker_stopwatch;
Request_T request;
Genome_T genome, genomealt;
+ /* Outbuffer_lines_T lines; -- For multithreaded, Output_thread_ordered and Output_thread_anyorder create lines */
Filestring_T fp, fp_failedinput;
Sequence_T queryseq;
int worker_jobid = 0;
@@ -4951,6 +4952,8 @@ worker_thread (void *data) {
if (fp_failedinput != NULL) {
Filestring_stringify(fp_failedinput);
}
+
+ /* For multithreaded, let Outbuffer_thread_ordered and Outbuffer_thread_anyordered call Outbuffer_lines_store */
Outbuffer_put_filestrings(outbuffer,fp,fp_failedinput);
if (worker_jobid % POOL_FREE_INTERVAL == 0) {
=====================================
src/gsnap.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gsnap.c 223772 2020-12-14 19:14:33Z twu $";
+static char rcsid[] = "$Id: gsnap.c 223812 2021-02-14 00:01:36Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -1209,8 +1209,7 @@ single_thread () {
}
/* Previously called Outbuffer_print_filestrings */
- if (Outbuffer_lines_store(lines,&fp,&fp_failedinput,&fp_failedinput_1,&fp_failedinput_2) >
- output_buffer_size) {
+ if (Outbuffer_lines_store(lines,&fp,&fp_failedinput,&fp_failedinput_1,&fp_failedinput_2) > output_buffer_size) {
Outbuffer_lines_print(lines);
}
@@ -1300,6 +1299,7 @@ single_thread () {
static void *
worker_thread (void *data) {
Request_T request;
+ /* Outbuffer_lines_T lines; -- For multithreaded, Output_thread_ordered and Output_thread_anyorder create lines */
Filestring_T fp, fp_failedinput, fp_failedinput_1, fp_failedinput_2;
Shortread_T queryseq1;
Stopwatch_T worker_stopwatch;
@@ -1423,6 +1423,8 @@ worker_thread (void *data) {
if (fp_failedinput_2 != NULL) {
Filestring_stringify(fp_failedinput_2);
}
+
+ /* For multithreaded, let Outbuffer_thread_ordered and Outbuffer_thread_anyordered call Outbuffer_lines_store */
Outbuffer_put_filestrings(outbuffer,fp,fp_failedinput,fp_failedinput_1,fp_failedinput_2);
if (worker_jobid % POOL_FREE_INTERVAL == 0) {
@@ -3658,12 +3660,6 @@ main (int argc, char *argv[]) {
FREE(dbversion);
chromosome_iit = chromosome_iit_setup(&genomelength,&nchromosomes,&circular_typeint,&any_circular_p,&circularp,
genomesubdir,genome_fileroot);
- Outbuffer_setup(argc,argv,optind,chromosome_iit,any_circular_p,
- nthreads,orderedp,quiet_if_excessive_p,
- output_type,sam_headers_p,sam_read_group_id,sam_read_group_name,
- sam_read_group_library,sam_read_group_platform,
- paired_end_p,appendp,output_file,split_output_root,failedinput_root);
-
if (transcriptome_dbroot != NULL) {
if (user_transcriptomedir == NULL && user_genomedir != NULL) {
@@ -3692,6 +3688,13 @@ main (int argc, char *argv[]) {
return 0;
}
+
+ Outbuffer_setup(argc,argv,optind,chromosome_iit,any_circular_p,
+ nthreads,orderedp,quiet_if_excessive_p,
+ output_type,sam_headers_p,sam_read_group_id,sam_read_group_name,
+ sam_read_group_library,sam_read_group_platform,
+ paired_end_p,appendp,output_file,split_output_root,failedinput_root);
+
outbuffer = Outbuffer_new(output_buffer_size,nread);
Inbuffer_set_outbuffer(inbuffer,outbuffer);
=====================================
src/outbuffer.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: outbuffer.c 223787 2020-12-16 16:18:27Z twu $";
+static char rcsid[] = "$Id: outbuffer.c 223814 2021-02-14 17:59:44Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -39,7 +39,11 @@ static char rcsid[] = "$Id: outbuffer.c 223787 2020-12-16 16:18:27Z twu $";
fewer system calls. */
#define OUTPUTLEN 65536
-#define USE_WRITE 0 /* Use write instead of fwrite. May not be portable. */
+
+/* Use write instead of fwrite. May not be portable, and is als not
+ thread-safe, so it can cause a race condition where alignment
+ output is printed before headers. Therefore, do not use */
+/* #define USE_WRITE 0 */
/* sam-to-bam conversions always need the headers */
#define SAM_HEADERS_ON_EMPTY_FILES 1
@@ -520,10 +524,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
buffer_outputs[split_output] = (char *) MALLOC_KEEP(OUTPUTLEN*sizeof(char));
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -535,10 +539,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
buffer_outputs[split_output] = (char *) MALLOC_KEEP(OUTPUTLEN*sizeof(char));
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -549,10 +553,10 @@ touch_all_single_outputs (FILE **outputs, char *split_output_root, bool appendp)
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
buffer_outputs[split_output] = (char *) MALLOC_KEEP(OUTPUTLEN*sizeof(char));
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -571,10 +575,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)
while (split_output <= N_SPLIT_OUTPUTS_STD) {
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -585,10 +589,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)
while (split_output <= N_SPLIT_OUTPUTS_TOCIRC) {
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -598,10 +602,10 @@ touch_all_paired_outputs (FILE **outputs, char *split_output_root, bool appendp)
while (split_output <= N_SPLIT_OUTPUTS) {
if (outputs[split_output] == NULL) {
outputs[split_output] = SAM_header_fopen(split_output,split_output_root,paired_end_p,appendp);
- setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
#ifdef SAM_HEADERS_ON_EMPTY_FILES
print_file_headers(outputs[split_output]);
#endif
+ setvbuf(outputs[split_output],buffer_outputs[split_output],_IOFBF,OUTPUTLEN);
}
split_output++;
}
@@ -815,8 +819,8 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput, Files
print_file_headers(stdout);
} else {
output = outputs[0] = SAM_header_fopen(/*split_output*/OUTPUT_FILE,output_file,paired_end_p,appendp);
- setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
print_file_headers(output);
+ setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
}
}
@@ -841,7 +845,7 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput, Files
return;
}
-#else
+#elif 0
void
Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput) {
SAM_split_output_type split_output;
@@ -863,12 +867,12 @@ Outbuffer_print_filestrings (Filestring_T fp, Filestring_T fp_failedinput) {
} else if ((output = outputs[0]) == NULL) {
if (output_file == NULL) {
output = outputs[0] = stdout;
- setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
print_file_headers(stdout);
+ setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
} else {
output = outputs[0] = SAM_header_fopen(/*split_output*/OUTPUT_FILE,output_file,paired_end_p,appendp);
- setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
print_file_headers(output);
+ setvbuf(outputs[0],buffer_outputs[0],_IOFBF,OUTPUTLEN);
}
}
@@ -936,6 +940,7 @@ Outbuffer_lines_store (Outbuffer_lines_T this, Filestring_T *fp, Filestring_T *f
#endif
) {
SAM_split_output_type split_output;
+ char *string;
if (split_output_root != NULL) {
split_output = Filestring_split_output(*fp);
@@ -955,18 +960,24 @@ Outbuffer_lines_store (Outbuffer_lines_T this, Filestring_T *fp, Filestring_T *f
this->nlines += 1;
if (*fp_failedinput != NULL) {
- this->lines_failedinput = List_push(this->lines_failedinput,(void *) Filestring_string(*fp_failedinput));
+ if ((string = Filestring_string(*fp_failedinput)) != NULL) {
+ this->lines_failedinput = List_push(this->lines_failedinput,(void *) string);
+ }
Filestring_free(&(*fp_failedinput),/*free_string_p*/false);
}
#ifdef GSNAP
if (*fp_failedinput_1 != NULL) {
- this->lines_failedinput_1 = List_push(this->lines_failedinput_1,(void *) Filestring_string(*fp_failedinput_1));
+ if ((string = Filestring_string(*fp_failedinput_1)) != NULL) {
+ this->lines_failedinput_1 = List_push(this->lines_failedinput_1,(void *) string);
+ }
Filestring_free(&(*fp_failedinput_1),/*free_string_p*/false);
}
if (*fp_failedinput_2 != NULL) {
- this->lines_failedinput_2 = List_push(this->lines_failedinput_2,(void *) Filestring_string(*fp_failedinput_2));
- Filestring_free(&(*fp_failedinput_1),/*free_string_p*/false);
+ if ((string = Filestring_string(*fp_failedinput_2)) != NULL) {
+ this->lines_failedinput_2 = List_push(this->lines_failedinput_2,(void *) string);
+ }
+ Filestring_free(&(*fp_failedinput_2),/*free_string_p*/false);
}
#endif
=====================================
src/output.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: output.c 223774 2020-12-14 19:16:04Z twu $";
+static char rcsid[] = "$Id: output.c 223811 2021-02-13 21:51:27Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -394,18 +394,13 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
Shortread_T queryseq1, queryseq2;
Stage3end_T *stage3array, stage3;
int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq;
+ bool print1p = false, print2p = false, single_end_p = false;
fp = Filestring_new(Request_id(request));
-
resulttype = Result_resulttype(result);
- if (resulttype == SINGLEEND_NOMAPPING) {
- if (failedinput_root == NULL) {
- *fp_failedinput = (Filestring_T) NULL;
- } else {
- *fp_failedinput = Filestring_new(Request_id(request));
- }
- *fp_failedinput_1 = *fp_failedinput_2 = (Filestring_T) NULL;
+ if (resulttype == SINGLEEND_NOMAPPING) {
+ single_end_p = true;
if (nofailsp == true) {
/* No output */
/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */
@@ -416,21 +411,10 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
Filestring_set_split_output(fp,OUTPUT_NM);
print_header_singleend(fp,request,/*translocationp*/false,/*npaths_primary*/0,/*npaths_altloc*/0);
FPRINTF(fp,"\n");
-
- if (failedinput_root != NULL) {
- queryseq1 = Request_queryseq1(request);
- Shortread_print_query_singleend(*fp_failedinput,queryseq1,/*headerseq*/queryseq1);
- }
}
} else if (resulttype == SINGLEEND_UNIQ) {
- if (failedinput_root == NULL) {
- *fp_failedinput = (Filestring_T) NULL;
- } else {
- *fp_failedinput = Filestring_new(Request_id(request));
- }
- *fp_failedinput_1 = *fp_failedinput_2 = (Filestring_T) NULL;
-
+ single_end_p = true;
if (failsonlyp == true) {
/* Skip */
/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */
@@ -441,6 +425,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
stage3 = stage3array[0];
+ print1p = true;
print_header_singleend(fp,request,/*translocationp*/false,npaths_primary,npaths_altloc);
Stage3end_print(fp,/*stage3pair*/NULL,stage3,
chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
@@ -453,13 +438,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
}
} else if (resulttype == SINGLEEND_TRANSLOC) {
- if (failedinput_root == NULL) {
- *fp_failedinput = (Filestring_T) NULL;
- } else {
- *fp_failedinput = Filestring_new(Request_id(request));
- }
- *fp_failedinput_1 = *fp_failedinput_2 = (Filestring_T) NULL;
-
+ single_end_p = true;
Filestring_set_split_output(fp,OUTPUT_UT);
stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
@@ -480,6 +459,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
} else {
queryseq1 = Request_queryseq1(request);
+ print1p = true;
print_header_singleend(fp,request,/*translocationp*/true,npaths_primary,npaths_altloc);
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
@@ -495,13 +475,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
}
} else if (resulttype == SINGLEEND_MULT) {
- if (failedinput_root == NULL) {
- *fp_failedinput = (Filestring_T) NULL;
- } else {
- *fp_failedinput = Filestring_new(Request_id(request));
- }
- *fp_failedinput_1 = *fp_failedinput_2 = (Filestring_T) NULL;
-
+ single_end_p = true;
stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
if (failsonlyp == true) {
@@ -523,6 +497,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
} else {
queryseq1 = Request_queryseq1(request);
+ print1p = true;
Filestring_set_split_output(fp,OUTPUT_UM);
print_header_singleend(fp,request,/*translocationp*/false,npaths_primary,npaths_altloc);
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
@@ -539,15 +514,6 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
}
} else if (resulttype == PAIREDEND_NOMAPPING) {
- *fp_failedinput = (Filestring_T) NULL;
- if (failedinput_root == NULL) {
- *fp_failedinput_1 = (Filestring_T) NULL;
- *fp_failedinput_2 = (Filestring_T) NULL;
- } else {
- *fp_failedinput_1 = Filestring_new(Request_id(request));
- *fp_failedinput_2 = Filestring_new(Request_id(request));
- }
-
if (nofailsp == true) {
/* No output */
/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */
@@ -557,30 +523,17 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
/* Stage3pair_print_end will call Filestring_set_split_output(), based on resulttype */
/* First end */
- Stage3pair_print_end(fp,*fp_failedinput_1,result,resulttype,'>',/*firstp*/true,chromosome_iit,
- /*queryseq*/queryseq1,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
- maxpaths_report,quiet_if_excessive_p,invert_first_p,quality_shift);
+ print1p = Stage3pair_print_end(fp,result,resulttype,'>',/*firstp*/true,chromosome_iit,
+ /*queryseq*/queryseq1,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
+ maxpaths_report,quiet_if_excessive_p,invert_first_p,quality_shift);
/* Second end */
- Stage3pair_print_end(fp,*fp_failedinput_2,result,resulttype,'<',/*firstp*/false,chromosome_iit,
- /*queryseq*/queryseq2,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
- maxpaths_report,quiet_if_excessive_p,invert_second_p,quality_shift);
-
- if (failedinput_root != NULL) {
- Shortread_print_query_pairedend(*fp_failedinput_1,*fp_failedinput_2,queryseq1,queryseq2);
- }
+ print2p = Stage3pair_print_end(fp,result,resulttype,'<',/*firstp*/false,chromosome_iit,
+ /*queryseq*/queryseq2,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
+ maxpaths_report,quiet_if_excessive_p,invert_second_p,quality_shift);
}
} else {
- *fp_failedinput = (Filestring_T) NULL;
- if (failedinput_root == NULL) {
- *fp_failedinput_1 = (Filestring_T) NULL;
- *fp_failedinput_2 = (Filestring_T) NULL;
- } else {
- *fp_failedinput_1 = Filestring_new(Request_id(request));
- *fp_failedinput_2 = Filestring_new(Request_id(request));
- }
-
if (failsonlyp == true) {
/* Unwanted success: skip */
/* Filestring_set_split_output(fp,OUTPUT_NONE); -- Already initialized to be OUTPUT_NONE */
@@ -591,14 +544,44 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput, Filestring_T *fp_fail
/* Stage3pair_print_end will call Filestring_set_split_output() based on resulttype */
/* First end */
- Stage3pair_print_end(fp,*fp_failedinput_1,result,resulttype,'>',/*firstp*/true,chromosome_iit,
- /*queryseq*/queryseq1,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
- maxpaths_report,quiet_if_excessive_p,invert_first_p,quality_shift);
+ print1p = Stage3pair_print_end(fp,result,resulttype,'>',/*firstp*/true,chromosome_iit,
+ /*queryseq*/queryseq1,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
+ maxpaths_report,quiet_if_excessive_p,invert_first_p,quality_shift);
/* Second end */
- Stage3pair_print_end(fp,*fp_failedinput_2,result,resulttype,'<',/*firstp*/false,chromosome_iit,
- /*queryseq*/queryseq2,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
- maxpaths_report,quiet_if_excessive_p,invert_second_p,quality_shift);
+ print2p = Stage3pair_print_end(fp,result,resulttype,'<',/*firstp*/false,chromosome_iit,
+ /*queryseq*/queryseq2,/*headerseq1*/queryseq1,/*headerseq2*/queryseq2,
+ maxpaths_report,quiet_if_excessive_p,invert_second_p,quality_shift);
+ }
+ }
+
+ if (single_end_p == true) {
+ *fp_failedinput_1 = *fp_failedinput_2 = (Filestring_T) NULL;
+ if (failedinput_root == NULL) {
+ *fp_failedinput = (Filestring_T) NULL;
+ } else if (print1p == true) {
+ *fp_failedinput = (Filestring_T) NULL;
+ } else {
+ queryseq1 = Request_queryseq1(request);
+ Shortread_print_query_singleend(*fp_failedinput,queryseq1,/*headerseq1*/queryseq1);
+ }
+
+ } else {
+ *fp_failedinput = (Filestring_T) NULL;
+ if (failedinput_root == NULL) {
+ *fp_failedinput_1 = (Filestring_T) NULL;
+ *fp_failedinput_2 = (Filestring_T) NULL;
+
+ } else if (print1p == true || print2p == true) {
+ *fp_failedinput_1 = (Filestring_T) NULL;
+ *fp_failedinput_2 = (Filestring_T) NULL;
+
+ } else {
+ *fp_failedinput_1 = Filestring_new(Request_id(request));
+ *fp_failedinput_2 = Filestring_new(Request_id(request));
+ queryseq1 = Request_queryseq1(request);
+ queryseq2 = Request_queryseq2(request);
+ Shortread_print_query_pairedend(*fp_failedinput_1,*fp_failedinput_2,queryseq1,queryseq2);
}
}
=====================================
src/resulthr.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: resulthr.c 223349 2020-10-28 02:49:25Z twu $";
+static char rcsid[] = "$Id: resulthr.c 223804 2021-02-13 17:17:31Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -297,7 +297,14 @@ Result_free (T *old) {
Stage3pair_T stage3pair;
switch ((*old)->resulttype) {
- case SINGLEEND_NOMAPPING: case PAIREDEND_NOMAPPING: break;
+ case SINGLEEND_NOMAPPING: case PAIREDEND_NOMAPPING:
+ /* It is possible to have results that are not printed because of various flags */
+ for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
+ stage3 = (*old)->array[i];
+ Stage3end_free(&stage3);
+ }
+ FREE_OUT((*old)->array);
+ break;
case SINGLEEND_UNIQ: case SINGLEEND_TRANSLOC: case SINGLEEND_MULT:
for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
=====================================
src/stage3hr.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3hr.c 223538 2020-11-15 12:03:08Z twu $";
+static char rcsid[] = "$Id: stage3hr.c 223808 2021-02-13 18:47:25Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -5368,9 +5368,9 @@ Stage3end_new_splice (int *found_score_overall, int *found_score_within_trims,
Substring_T substring1, substringN;
Junction_T junction;
- List_T transcripts;
- char *remap_sequence;
- int remap_seqlength;
+ /* List_T transcripts; */
+ /* char *remap_sequence; */
+ /* int remap_seqlength; */
double donor_prob, acceptor_prob;
#ifdef DEBUG0
Substring_T substring;
@@ -5706,9 +5706,9 @@ Stage3end_new_distant (int *found_score_overall, int *found_score_within_trims,
Substring_T donor, acceptor;
Junction_T junction;
- List_T transcripts;
- char *remap_sequence;
- int remap_seqlength;
+ /* List_T transcripts; */
+ /* char *remap_sequence; */
+ /* int remap_seqlength; */
#ifdef DEBUG0
Substring_T substring;
List_T p;
@@ -10074,18 +10074,17 @@ print_barcode_and_quality (Filestring_T fp, Shortread_T queryseq, bool invertp,
}
-void
-Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
- Result_T result, Resulttype_T resulttype,
+bool
+Stage3pair_print_end (Filestring_T fp, Result_T result, Resulttype_T resulttype,
char initchar, bool firstp, Univ_IIT_T chromosome_iit,
Shortread_T queryseq, Shortread_T headerseq1, Shortread_T headerseq2,
int maxpaths, bool quiet_if_excessive_p,
bool invertp, int quality_shift) {
+ bool printp = false, excessivep, translocationp;
Stage3pair_T *stage3pairarray, stage3pair;
T *stage3array, *stage3array_mate, this, hit5, hit3;
int npaths_primary, npaths_altloc, npaths_mate_primary, npaths_mate_altloc, pathnum;
int first_absmq, second_absmq;
- bool excessivep, translocationp;
if (resulttype == PAIREDEND_NOMAPPING) {
if (output_type != M8_OUTPUT) {
@@ -10099,7 +10098,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
FPRINTF(fp,"\n");
}
- /* If failedinput_root != NULL, then this case is handled by calling procedure */
} else if (resulttype == CONCORDANT_UNIQ) {
stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
@@ -10128,6 +10126,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
+ printp = true;
if (firstp == true) {
Stage3end_print(fp,stage3pair,hit5,
chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
@@ -10171,10 +10170,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
FPRINTF(fp,"\n");
}
- if (failedinput_root != NULL) {
- Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);
- }
-
} else {
if (output_type != M8_OUTPUT) {
print_query_header(fp,initchar,queryseq,invertp);
@@ -10187,6 +10182,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
+ printp = true;
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
@@ -10237,10 +10233,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
/* No further output */
FPRINTF(fp,"\n");
-
- if (failedinput_root != NULL) {
- Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);
- }
+ printp = false;
}
} else {
@@ -10255,6 +10248,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
+ printp = true;
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
@@ -10314,6 +10308,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
+ printp = true;
if (firstp == true) {
Stage3end_print(fp,stage3pair,hit5,
chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
@@ -10352,10 +10347,6 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
/* No further output */
FPRINTF(fp,"\n");
-
- if (failedinput_root != NULL) {
- Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);
- }
}
} else {
@@ -10370,6 +10361,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
+ printp = true;
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
@@ -10476,11 +10468,9 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
if (excessivep == true) {
/* No output */
- if (failedinput_root != NULL) {
- Shortread_print_query_singleend(fp_failedinput,queryseq,headerseq1);
- }
} else {
+ printp = true;
if (firstp == true) {
for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
this = stage3array[pathnum-1];
@@ -10507,7 +10497,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
}
}
- return;
+ return printp;
}
@@ -11433,9 +11423,9 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype
int querylength5 = hit5_orig->querylength;
int querylength3 = hit3_orig->querylength;
- char *remap_sequence;
- int remap_seqlength;
- List_T transcripts;
+ /* char *remap_sequence; */
+ /* int remap_seqlength; */
+ /* List_T transcripts; */
debug0(printf("\nStage3pair_new called with pairtype %s and chrnum %d, %d (effective %d, %d), expect_concordant_p %d\n",
=====================================
src/stage3hr.h
=====================================
@@ -1,4 +1,4 @@
-/* $Id: stage3hr.h 223538 2020-11-15 12:03:08Z twu $ */
+/* $Id: stage3hr.h 223808 2021-02-13 18:47:25Z twu $ */
#ifndef STAGE3HR_INCLUDED
#define STAGE3HR_INCLUDED
@@ -420,9 +420,8 @@ Stage3end_print_transcript_info (Filestring_T fp, Intlist_T trnums, Intlist_T tr
extern void
Stage3end_print_transcript_diff (Filestring_T fp, T hit, Intlist_T common_trnums, bool invertp);
-extern void
-Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
- Result_T result, Resulttype_T resulttype,
+extern bool
+Stage3pair_print_end (Filestring_T fp, Result_T result, Resulttype_T resulttype,
char initchar, bool firstp, Univ_IIT_T chromosome_iit,
Shortread_T queryseq, Shortread_T headerseq1, Shortread_T headerseq2,
int maxpaths, bool quiet_if_excessive_p,
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/0ba0084d34b8453a7c19ded1b3b6bf3e3743d358
--
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/0ba0084d34b8453a7c19ded1b3b6bf3e3743d358
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