From 966b93b2433fe4ef708c5d0805f496b1cb4feca4 Mon Sep 17 00:00:00 2001
From: Jacob Morrison <Jacob.Morrison@vai.org>
Date: Mon, 6 Nov 2023 14:56:32 -0500
Subject: [PATCH] make bc compatible with umi-tools format

---
 src/bc.c | 26 ++++++++++++++++----------
 src/bc.h | 11 ++++++++++-
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/src/bc.c b/src/bc.c
index a268605..04d0eff 100644
--- a/src/bc.c
+++ b/src/bc.c
@@ -65,14 +65,16 @@ int prepare_read_se(kseq_t *k, kstring_t *s, bc_conf_t *conf) {
         }
     }
 
+    // Remove "/1" or "/2" from the end of the read name
+    remove_read_number(k);
+
     // Create read entry
     // NOTE: This assumes there was a FASTQ comment, it may be worth it to look into how
     //       to handle cases where there aren't comments to start with
     ksprintf(
         s,
-        "@%s %s:%.*s\n%.*s%s\n+\n%.*s%s\n",
-        k->name.s, k->comment.s,
-        conf->bc_length, k->seq.s+conf->bc_start,
+        "@%s_%.*s_AAAAAAAA %s\n%.*s%s\n+\n%.*s%s\n",
+        k->name.s, conf->bc_length, k->seq.s+conf->bc_start, k->comment.s,
         conf->bc_start, k->seq.s, k->seq.s+conf->bc_start+conf->bc_length,
         conf->bc_start, k->qual.s, k->qual.s+conf->bc_start+conf->bc_length
     );
@@ -112,14 +114,17 @@ int prepare_read_pe(kseq_t *k1, kseq_t *k2, kstring_t *s1, kstring_t *s2, bc_con
         }
     }
 
+    // Remove "/1" or "/2" from the end of the read name
+    remove_read_number(k_has_bc);
+    remove_read_number(k_not_bc);
+
     // Create entry for read with barcode
     // NOTE: This assumes there was a FASTQ comment, it may be worth it to look into how
     //       to handle cases where there aren't comments to start with
     ksprintf(
         s_has_bc,
-        "@%s %s:%.*s\n%.*s%s\n+\n%.*s%s\n",
-        k_has_bc->name.s, k_has_bc->comment.s,
-        conf->bc_length, k_has_bc->seq.s+conf->bc_start,
+        "@%s_%.*s_AAAAAAAA %s\n%.*s%s\n+\n%.*s%s\n",
+        k_has_bc->name.s, conf->bc_length, k_has_bc->seq.s+conf->bc_start, k_has_bc->comment.s,
         conf->bc_start, k_has_bc->seq.s, k_has_bc->seq.s+conf->bc_start+conf->bc_length,
         conf->bc_start, k_has_bc->qual.s, k_has_bc->qual.s+conf->bc_start+conf->bc_length
     );
@@ -129,9 +134,8 @@ int prepare_read_pe(kseq_t *k1, kseq_t *k2, kstring_t *s1, kstring_t *s2, bc_con
     //       to handle cases where there aren't comments to start with
     ksprintf(
         s_not_bc,
-        "@%s %s:%.*s\n%s\n+\n%s\n",
-        k_not_bc->name.s, k_not_bc->comment.s,
-        conf->bc_length, k_has_bc->seq.s+conf->bc_start,
+        "@%s_%.*s_AAAAAAAA %s\n%s\n+\n%s\n",
+        k_not_bc->name.s, conf->bc_length, k_has_bc->seq.s+conf->bc_start, k_not_bc->comment.s,
         k_not_bc->seq.s, k_not_bc->qual.s
     );
 
@@ -231,7 +235,9 @@ static void usage() {
     fprintf(stderr, "General Options:\n");
     fprintf(stderr, "    -h, --help             This help\n");
     fprintf(stderr, "\n");
-    fprintf(stderr, "Note: When writing to stdout, reads 1 and 2 will alternate (i.e., are interleaved)\n");
+    fprintf(stderr, "Note 1: When writing to stdout, reads 1 and 2 will alternate (i.e., are interleaved)\n");
+    fprintf(stderr, "Note 2: Also adds an artificial UMI (AAAAAAAA) for compatibility purposes and to serve\n");
+    fprintf(stderr, "        as a placeholder for future UMI work\n");
     fprintf(stderr, "\n");
 }
 
diff --git a/src/bc.h b/src/bc.h
index 055934d..416563e 100644
--- a/src/bc.h
+++ b/src/bc.h
@@ -37,7 +37,7 @@
 KSEQ_INIT(gzFile, gzread)
 
 // Number of extra bytes to allocate
-#define N_EXTRA 32
+#define N_EXTRA 64
 
 // uint8_t should be large enough for now, but if barcodes start to occur
 // in locations further in from the start of the read or barcode lengths
@@ -58,6 +58,15 @@ static inline void bc_conf_init(bc_conf_t *conf) {
 
 gzFile setup_output(const char *ofile, uint8_t read_num);
 
+// Remove "/1" and "/2" from read name
+static inline void remove_read_number(kseq_t *k) {
+    size_t len = k->name.l;
+    if (len > 2 && k->name.s[len-2] == '/' && (k->name.s[len-1] == '1' || k->name.s[len-1] == '2')) {
+        k->name.s[len-2] = '\0';
+        k->name.l = len-2;
+    }
+}
+
 int prepare_read_se(kseq_t *k, kstring_t *s, bc_conf_t *conf);
 
 void extract_barcodes(bc_conf_t *conf, kseq_t *ks1, kseq_t *ks2, gzFile oh1, gzFile oh2);