From 8125d5b05449b81c2979a10359e26f310d79d799 Mon Sep 17 00:00:00 2001
From: John Didion <github@didion.net>
Date: Tue, 21 Oct 2014 16:37:53 -0400
Subject: [PATCH 1/2] Orphan quality and length thresholds

Added two new options, -Q and -L, to specify quality and length
thresholds, respectively, for orphaned reads, i.e. read pairs where one
mate but not both fails the initial quality check.
---
 src/trim_paired.c | 130 +++++++++++++++++++++++++++++++++++-----------
 1 file changed, 99 insertions(+), 31 deletions(-)

diff --git a/src/trim_paired.c b/src/trim_paired.c
index f63b877..13f4597 100644
--- a/src/trim_paired.c
+++ b/src/trim_paired.c
@@ -14,7 +14,10 @@ __KS_GETUNTIL(gzread, BUFFER_SIZE)
 __KSEQ_READ
 
 int paired_qual_threshold = 20;
+int orphan_qual_threshold = -1;
 int paired_length_threshold = 20;
+int orphan_length_threshold = -1;
+int recheck_orphans = 1;
 
 static struct option paired_long_options[] = {
     {"qual-type", required_argument, 0, 't'},
@@ -26,7 +29,9 @@ static struct option paired_long_options[] = {
     {"output-single", optional_argument, 0, 's'},
     {"output-combo", optional_argument, 0, 'm'},
     {"qual-threshold", optional_argument, 0, 'q'},
+    {"orphan-qual-threshold", optional_argument, 0, 'Q'},
     {"length-threshold", optional_argument, 0, 'l'},
+    {"orphan-length-threshold", optional_argument, 0, 'L'},
     {"no-fiveprime", optional_argument, 0, 'x'},
     {"truncate-n", optional_argument, 0, 'n'},
     {"gzip-output", optional_argument, 0, 'g'},
@@ -62,7 +67,9 @@ Global options\n\
 -t, --qual-type, Type of quality values (solexa (CASAVA < 1.3), illumina (CASAVA 1.3 to 1.7), sanger (which is CASAVA >= 1.8)) (required)\n");
     fprintf(stderr, "-s, --output-single, Output trimmed singles fastq file\n\
 -q, --qual-threshold, Threshold for trimming based on average quality in a window. Default 20.\n\
+-Q, --orphan-qual-threshold, Quality threshold to use for retaining a single mate if one (but not both) mate fails the paired-end quality threshold. Defaults to the value specified for --qual-threshold.\n\
 -l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.\n\
+-L, --orphan-length-threshold, Length threshold to use for retaining a single mate if one (but not both) mate fails the paired-end length threshold. Defaults to the value specified for --length-threshold.\n\
 -x, --no-fiveprime, Don't do five prime trimming.\n\
 -n, --truncate-n, Truncate sequences at position of first N.\n");
 
@@ -118,10 +125,10 @@ int paired_main(int argc, char *argv[]) {
     int combo_all=0;
     int combo_s=0;
     int total=0;
-
+    
     while (1) {
         int option_index = 0;
-        optc = getopt_long(argc, argv, "df:r:c:t:o:p:m:M:s:q:l:xng", paired_long_options, &option_index);
+        optc = getopt_long(argc, argv, "df:r:c:t:o:p:m:M:s:q:l:Q:L:xng", paired_long_options, &option_index);
 
         if (optc == -1)
             break;
@@ -189,7 +196,15 @@ int paired_main(int argc, char *argv[]) {
                 return EXIT_FAILURE;
             }
             break;
-
+        
+        case 'Q':
+            orphan_qual_threshold = atoi(optarg);
+            if (orphan_qual_threshold < 0) {
+                fprintf(stderr, "Orphan quality threshold must be >= 0\n");
+                return EXIT_FAILURE;
+            }
+            break;
+            
         case 'l':
             paired_length_threshold = atoi(optarg);
             if (paired_length_threshold < 0) {
@@ -198,6 +213,14 @@ int paired_main(int argc, char *argv[]) {
             }
             break;
 
+        case 'L':
+            orphan_length_threshold = atoi(optarg);
+            if (orphan_length_threshold < 0) {
+                fprintf(stderr, "Orphan length threshold must be >= 0\n");
+                return EXIT_FAILURE;
+            }
+            break;
+
         case 'x':
             no_fiveprime = 1;
             break;
@@ -241,6 +264,20 @@ int paired_main(int argc, char *argv[]) {
         paired_usage(EXIT_FAILURE, "****Error: Must have either -f OR -c argument.");
     }
 
+    /* set orphan length and quality thresholds to paired thresholds if unset */
+    if ((orphan_qual_threshold == -1 || orphan_qual_threshold == paired_qual_threshold) && 
+            (orphan_length_threshold == -1 || orphan_length_threshold == paired_length_threshold)) {
+        recheck_orphans = 0;
+    }
+    else {
+        if (orphan_qual_threshold == -1) {
+            orphan_qual_threshold = paired_qual_threshold;
+        }
+        if (orphan_length_threshold == -1) {
+            orphan_length_threshold = paired_length_threshold;
+        }
+    }
+    
     if (infnc) {      /* using combined input file */
 
         if (infn1 || infn2 || outfn1 || outfn2) {
@@ -411,45 +448,76 @@ int paired_main(int argc, char *argv[]) {
         /* if only one sequence passed filter, then put its record in singles and discard the other */
         /* or put an "N" record in if that option was chosen. */
         else if (p1cut->three_prime_cut >= 0 && p2cut->three_prime_cut < 0) {
-            if (!gzip_output) {
-                if (combo_all) {
-                    print_record (combo, fqrec1, p1cut);
-                    print_record_N (combo, fqrec2, qualtype);
-                } else {
-                    print_record (single, fqrec1, p1cut);
+            int write_orphan = 1;
+            
+            if (recheck_orphans) {
+                p1cut = sliding_window(fqrec1, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, debug);
+                if (p1cut->three_prime_cut < 0) {
+                    if (debug) printf("p1 orhpan discarded");
+                    write_orphan = 0;
                 }
-            } else {
-                if (combo_all) {
-                    print_record_gzip (combo_gzip, fqrec1, p1cut);
-                    print_record_N_gzip (combo_gzip, fqrec2, qualtype);
+                else if (debug) printf("p1 orhpan retained");
+            }
+            
+            if (write_orphan) {
+                if (!gzip_output) {
+                    if (combo_all) {
+                        print_record (combo, fqrec1, p1cut);
+                        print_record_N (combo, fqrec2, qualtype);
+                    } else {
+                        print_record (single, fqrec1, p1cut);
+                    }
                 } else {
-                    print_record_gzip (single_gzip, fqrec1, p1cut);
+                    if (combo_all) {
+                        print_record_gzip (combo_gzip, fqrec1, p1cut);
+                        print_record_N_gzip (combo_gzip, fqrec2, qualtype);
+                    } else {
+                        print_record_gzip (single_gzip, fqrec1, p1cut);
+                    }
                 }
-            }
 
-            kept_s1++;
-            discard_s2++;
+                kept_s1++;
+                discard_s2++;
+            }
+            else {
+                discard_s2 += 2;
+            }
         }
 
         else if (p1cut->three_prime_cut < 0 && p2cut->three_prime_cut >= 0) {
-            if (!gzip_output) {
-                if (combo_all) {
-                    print_record_N (combo, fqrec1, qualtype);
-                    print_record (combo, fqrec2, p2cut);
-                } else {
-                    print_record (single, fqrec2, p2cut);
+            int write_orphan = 1;
+            
+            if (recheck_orphans) {
+                p2cut = sliding_window(fqrec2, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, debug);
+                if (p2cut->three_prime_cut < 0) {
+                    if (debug) printf("p2 orhpan discarded");
+                    write_orphan = 0;
                 }
-            } else {
-                if (combo_all) {
-                    print_record_N_gzip (combo_gzip, fqrec1, qualtype);
-                    print_record_gzip (combo_gzip, fqrec2, p2cut);
+                else if (debug) printf("p2 orhpan retained");
+            }
+            
+            if (write_orphan) {
+                if (!gzip_output) {
+                    if (combo_all) {
+                        print_record_N (combo, fqrec1, qualtype);
+                        print_record (combo, fqrec2, p2cut);
+                    } else {
+                        print_record (single, fqrec2, p2cut);
+                    }
                 } else {
-                    print_record_gzip (single_gzip, fqrec2, p2cut);
+                    if (combo_all) {
+                        print_record_N_gzip (combo_gzip, fqrec1, qualtype);
+                        print_record_gzip (combo_gzip, fqrec2, p2cut);
+                    } else {
+                        print_record_gzip (single_gzip, fqrec2, p2cut);
+                    }
                 }
+                kept_s2++;
+                discard_s1++;
+            }
+            else {
+                discard_s2 += 2;
             }
-
-            kept_s2++;
-            discard_s1++;
 
         } else {
 

From 482e83988a6ee18824b4c7ea391bdc644197dea5 Mon Sep 17 00:00:00 2001
From: "Didion, John (NIH/NHGRI) [F]" <john.didion@nih.gov>
Date: Mon, 15 Jun 2015 11:29:51 -0400
Subject: [PATCH 2/2] add parameters for truncating reads

---
 foo               | Bin 0 -> 31592 bytes
 src/sickle.h      |   2 +-
 src/sliding.c     |  25 +++++++++++++++++--
 src/trim_paired.c |  62 +++++++++++++++++++++++++++++++++++-----------
 src/trim_single.c |   9 +++++--
 5 files changed, 78 insertions(+), 20 deletions(-)
 create mode 100755 foo

diff --git a/foo b/foo
new file mode 100755
index 0000000000000000000000000000000000000000..736b20793b8b063b5561ad4b1c68acf3a7fd12a3
GIT binary patch
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diff --git a/src/sickle.h b/src/sickle.h
index e7b679c..d30df14 100644
--- a/src/sickle.h
+++ b/src/sickle.h
@@ -96,6 +96,6 @@ typedef struct __cutsites_ {
 /* Function Prototypes */
 int single_main (int argc, char *argv[]);
 int paired_main (int argc, char *argv[]);
-cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int debug);
+cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int trunc_size, int debug);
 
 #endif /*SICKLE_H*/
diff --git a/src/sliding.c b/src/sliding.c
index 7573106..056b7a8 100644
--- a/src/sliding.c
+++ b/src/sliding.c
@@ -32,8 +32,11 @@ int get_quality_num (char qualchar, int qualtype, kseq_t *fqrec, int pos) {
 }
 
 
-cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int debug) {
-
+cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int trunc_size, int debug) {
+    if (trunc_size >= 0 && trunc_size < length_threshold) {
+        trunc_size = length_threshold;
+    }
+    
 	int window_size = (int) (0.1 * fqrec->seq.l);
 	int i,j;
 	int window_start=0;
@@ -130,6 +133,24 @@ cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int
 
     if (debug) printf ("\n\n");
 
+    /* if trunc_size is less than read length, remove equal number of bases from each side */
+    /* TODO: this should acutally remove bases based on quality */
+    
+    
+    if (trunc_size >= 0) {
+        int side = 0;
+        while (trunc_size < three_prime_cut - five_prime_cut) {
+            if (side == 0) {
+                five_prime_cut++;
+                side = 1;
+            }
+            else {
+                three_prime_cut--;
+                side = 0;
+            }
+        }
+    }
+
 	retvals = (cutsites*) malloc (sizeof(cutsites));
 	retvals->three_prime_cut = three_prime_cut;
 	retvals->five_prime_cut = five_prime_cut;
diff --git a/src/trim_paired.c b/src/trim_paired.c
index 13f4597..c138830 100644
--- a/src/trim_paired.c
+++ b/src/trim_paired.c
@@ -26,6 +26,7 @@ static struct option paired_long_options[] = {
     {"pe-combo", optional_argument, 0, 'c'},
     {"output-pe1", optional_argument, 0, 'o'},
     {"output-pe2", optional_argument, 0, 'p'},
+    {"output-all", optional_argument, 0, 'a'},
     {"output-single", optional_argument, 0, 's'},
     {"output-combo", optional_argument, 0, 'm'},
     {"qual-threshold", optional_argument, 0, 'q'},
@@ -34,6 +35,7 @@ static struct option paired_long_options[] = {
     {"orphan-length-threshold", optional_argument, 0, 'L'},
     {"no-fiveprime", optional_argument, 0, 'x'},
     {"truncate-n", optional_argument, 0, 'n'},
+    {"truncate-size", optional_argument, 0, 'N'},
     {"gzip-output", optional_argument, 0, 'g'},
     {"output-combo-all", optional_argument, 0, 'M'},
     {"quiet", optional_argument, 0, 'z'},
@@ -56,7 +58,8 @@ Paired-end separated reads\n\
 -f, --pe-file1, Input paired-end forward fastq file (Input files must have same number of records)\n\
 -r, --pe-file2, Input paired-end reverse fastq file\n\
 -o, --output-pe1, Output trimmed forward fastq file\n\
--p, --output-pe2, Output trimmed reverse fastq file. Must use -s option.\n\n\
+-p, --output-pe2, Output trimmed reverse fastq file. Must use -s option.\n\
+-a, --output-all, Output all pairs with at least one surviving reads, with a discarded read written to output file as a single N.\n\n\
 Paired-end interleaved reads\n\
 ----------------------------\n");
     fprintf(stderr,"-c, --pe-combo, Combined (interleaved) input paired-end fastq\n\
@@ -71,7 +74,8 @@ Global options\n\
 -l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.\n\
 -L, --orphan-length-threshold, Length threshold to use for retaining a single mate if one (but not both) mate fails the paired-end length threshold. Defaults to the value specified for --length-threshold.\n\
 -x, --no-fiveprime, Don't do five prime trimming.\n\
--n, --truncate-n, Truncate sequences at position of first N.\n");
+-n, --truncate-n, Truncate sequences at position of first N.\n\
+-N, --truncate-size, Truncate sequences at a maximum length.\n");
 
 
     fprintf(stderr, "-g, --gzip-output, Output gzipped files.\n--quiet, do not output trimming info\n\
@@ -121,14 +125,16 @@ int paired_main(int argc, char *argv[]) {
     int quiet = 0;
     int no_fiveprime = 0;
     int trunc_n = 0;
+    int trunc_size = -1;
     int gzip_output = 0;
+    int split_all = 0;
     int combo_all=0;
     int combo_s=0;
     int total=0;
     
     while (1) {
         int option_index = 0;
-        optc = getopt_long(argc, argv, "df:r:c:t:o:p:m:M:s:q:l:Q:L:xng", paired_long_options, &option_index);
+        optc = getopt_long(argc, argv, "df:r:c:t:o:p:m:M:s:q:l:Q:L:xnga", paired_long_options, &option_index);
 
         if (optc == -1)
             break;
@@ -171,7 +177,11 @@ int paired_main(int argc, char *argv[]) {
             outfn2 = (char *) malloc(strlen(optarg) + 1);
             strcpy(outfn2, optarg);
             break;
-
+        
+        case 'a':
+            split_all = 1;
+            break;
+        
         case 'm':
             outfnc = (char *) malloc(strlen(optarg) + 1);
             strcpy(outfnc, optarg);
@@ -228,7 +238,9 @@ int paired_main(int argc, char *argv[]) {
         case 'n':
             trunc_n = 1;
             break;
-
+        case 'N':
+            trunc_size = atoi(optarg);
+            break;    
         case 'g':
             gzip_output = 1;
             break;
@@ -278,6 +290,10 @@ int paired_main(int argc, char *argv[]) {
         }
     }
     
+    if (split_all) {
+        sfn = "";
+    }
+    
     if (infnc) {      /* using combined input file */
 
         if (infn1 || infn2 || outfn1 || outfn2) {
@@ -321,7 +337,7 @@ int paired_main(int argc, char *argv[]) {
 
     } else {     /* using forward and reverse input files */
 
-        if (infn1 && (!infn2 || !outfn1 || !outfn2 || !sfn)) {
+        if (infn1 && (!infn2 || !outfn1 || !outfn2 || (!sfn && !split_all))) {
             paired_usage(EXIT_FAILURE, "****Error: Using the -f option means you must have the -r, -o, -p, and -s options.");
         }
 
@@ -378,7 +394,7 @@ int paired_main(int argc, char *argv[]) {
     }
 
     /* get singles output file handle */
-    if (sfn && !combo_all) {
+    if (sfn && !combo_all && !split_all) {
         if (!gzip_output) {
             single = fopen(sfn, "w");
             if (!single) {
@@ -411,8 +427,8 @@ int paired_main(int argc, char *argv[]) {
             break;
         }
 
-        p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
-        p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
+        p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, trunc_size, debug);
+        p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, trunc_size, debug);
         total += 2;
 
         if (debug) printf("p1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);
@@ -451,7 +467,7 @@ int paired_main(int argc, char *argv[]) {
             int write_orphan = 1;
             
             if (recheck_orphans) {
-                p1cut = sliding_window(fqrec1, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, debug);
+                p1cut = sliding_window(fqrec1, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, trunc_size, debug);
                 if (p1cut->three_prime_cut < 0) {
                     if (debug) printf("p1 orhpan discarded");
                     write_orphan = 0;
@@ -464,14 +480,22 @@ int paired_main(int argc, char *argv[]) {
                     if (combo_all) {
                         print_record (combo, fqrec1, p1cut);
                         print_record_N (combo, fqrec2, qualtype);
-                    } else {
+                    } else if (split_all) {
+                        print_record(outfile1, fqrec1, p1cut);
+                        print_record_N(outfile2, fqrec2, qualtype);
+                    }
+                    else {
                         print_record (single, fqrec1, p1cut);
                     }
                 } else {
                     if (combo_all) {
                         print_record_gzip (combo_gzip, fqrec1, p1cut);
                         print_record_N_gzip (combo_gzip, fqrec2, qualtype);
-                    } else {
+                    } else if (split_all) {
+                        print_record_gzip(outfile1, fqrec1, p1cut);
+                        print_record_N_gzip(outfile2, fqrec2, qualtype);
+                    }
+                    else {
                         print_record_gzip (single_gzip, fqrec1, p1cut);
                     }
                 }
@@ -488,7 +512,7 @@ int paired_main(int argc, char *argv[]) {
             int write_orphan = 1;
             
             if (recheck_orphans) {
-                p2cut = sliding_window(fqrec2, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, debug);
+                p2cut = sliding_window(fqrec2, qualtype, orphan_length_threshold, orphan_qual_threshold, no_fiveprime, trunc_n, trunc_size, debug);
                 if (p2cut->three_prime_cut < 0) {
                     if (debug) printf("p2 orhpan discarded");
                     write_orphan = 0;
@@ -501,14 +525,22 @@ int paired_main(int argc, char *argv[]) {
                     if (combo_all) {
                         print_record_N (combo, fqrec1, qualtype);
                         print_record (combo, fqrec2, p2cut);
-                    } else {
+                    } else if (split_all) {
+                        print_record_N(outfile1, fqrec1, qualtype);
+                        print_record(outfile2, fqrec2, p2cut);
+                    }
+                    else {
                         print_record (single, fqrec2, p2cut);
                     }
                 } else {
                     if (combo_all) {
                         print_record_N_gzip (combo_gzip, fqrec1, qualtype);
                         print_record_gzip (combo_gzip, fqrec2, p2cut);
-                    } else {
+                    } else if (split_all) {
+                        print_record_N_gzip(outfile1, fqrec1, qualtype);
+                        print_record_gzip(outfile2, fqrec2, p2cut);
+                    }
+                    else {
                         print_record_gzip (single_gzip, fqrec2, p2cut);
                     }
                 }
diff --git a/src/trim_single.c b/src/trim_single.c
index 44fe013..e182c04 100644
--- a/src/trim_single.c
+++ b/src/trim_single.c
@@ -23,6 +23,7 @@ static struct option single_long_options[] = {
     {"length-threshold", optional_argument, 0, 'l'},
     {"no-fiveprime", optional_argument, 0, 'x'},
     {"discard-n", optional_argument, 0, 'n'},
+    {"trunc-size", optional_argument, 0, 'N'},
     {"gzip-output", optional_argument, 0, 'g'},
     {"quiet", optional_argument, 0, 'z'},
     {GETOPT_HELP_OPTION_DECL},
@@ -43,6 +44,7 @@ Options:\n\
 -l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.\n\
 -x, --no-fiveprime, Don't do five prime trimming.\n\
 -n, --trunc-n, Truncate sequences at position of first N.\n\
+-N, --truncate-size, Truncate sequences at a maximum length.\n\
 -g, --gzip-output, Output gzipped files.\n\
 --quiet, Don't print out any trimming information\n\
 --help, display this help and exit\n\
@@ -71,6 +73,7 @@ int single_main(int argc, char *argv[]) {
     int quiet = 0;
     int no_fiveprime = 0;
     int trunc_n = 0;
+    int trunc_size = -1;
     int gzip_output = 0;
     int total=0;
 
@@ -131,7 +134,9 @@ int single_main(int argc, char *argv[]) {
         case 'n':
             trunc_n = 1;
             break;
-
+        case 'N':
+            trunc_size = atoi(optarg);
+            break;
         case 'g':
             gzip_output = 1;
             break;
@@ -192,7 +197,7 @@ int single_main(int argc, char *argv[]) {
 
     while ((l = kseq_read(fqrec)) >= 0) {
 
-        p1cut = sliding_window(fqrec, qualtype, single_length_threshold, single_qual_threshold, no_fiveprime, trunc_n, debug);
+        p1cut = sliding_window(fqrec, qualtype, single_length_threshold, single_qual_threshold, no_fiveprime, trunc_n, trunc_size, debug);
         total++;
 
         if (debug) printf("P1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);