make align work with umi-tools compatible barcode format

lib/aln/align.c

@@ -153,7 +153,7 @@ static void *process(void *shared, int step, void *_data) {
   } else if (step == 2) {
     for (i = 0; i < data->n_seqs; ++i) {
       if (data->seqs[i].sam) err_fputs(data->seqs[i].sam, stdout);
-      free(data->seqs[i].name); free(data->seqs[i].comment); free(data->seqs[i].barcode);
+      free(data->seqs[i].name); free(data->seqs[i].comment); free(data->seqs[i].barcode); free(data->seqs[i].umi);
       free(data->seqs[i].seq0); free(data->seqs[i].qual); free(data->seqs[i].sam);
       /* bisulfite free, the pointers can be NULL */
       free(data->seqs[i].bisseq[0]);
@@ -257,7 +257,7 @@ int usage(mem_opt_t *opt) {
     fprintf(stderr, "    -S              Skip mate rescue\n");
     fprintf(stderr, "    -P              Skip pairing - mate rescue performed unless -S also given\n");
     fprintf(stderr, "    -e              Discard full-length exact matches\n");
-    fprintf(stderr, "    -9              Extract barcode from read comment\n");
+    fprintf(stderr, "    -9              Extract barcode and UMI from read name\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Scoring options:\n");
     fprintf(stderr, "    -A INT          Score for a sequence match, scales options -TdBOELU unless\n");

lib/aln/bwa.c

@@ -767,12 +767,38 @@ static void bis_kseq2bseq1(const kseq_t *ks, bseq1_t *s, uint8_t has_bc)
 { // TODO: it would be better to allocate one chunk of memory, but probably it does not matter in practice
   s->name = strdup(ks->name.s);
   s->comment = ks->comment.l? strdup(ks->comment.s) : 0;
-  if (has_bc && ks->comment.l) {
-    // No checks are performed here, so we have to rely on the user to have done the proper
+  if (has_bc) {
+    // Minimal checks are performed here, so we have to rely on the user to have done the proper
     // preprocessing before processing with barcodes
-    s->barcode = strdup(strrchr(ks->comment.s, ':') + 1);
+    char *temp_string = strdup(ks->name.s);
+    char *temp_tok = NULL;
+    char *bc = NULL;
+    char *umi = NULL;
+
+    // Pull out first entry
+    temp_tok = strtok(temp_string, "_");
+
+    if (!temp_tok) {
+        fprintf(stderr, "[W::%s] barcode and UMI extraction requested but could not include be extracted\n", __func__);
+    }
+
+    // barcode
+    bc = strtok(NULL, "_");
+
+    // umi
+    umi = strtok(NULL, "_");
+
+    while ((temp_tok = strtok(NULL, "_")) != NULL) {
+        bc = umi;
+        umi = temp_tok;
+    }
+
+    s->barcode = strdup(bc);
+    s->umi = strdup(umi);
+    free(temp_string);
   } else {
       s->barcode = 0;
+      s->umi = 0;
   }
   s->seq = (uint8_t*) strdup(ks->seq.s);
   s->seq0 = s->seq;

lib/aln/bwa.h

@@ -51,7 +51,7 @@ typedef struct {
 
 typedef struct {
    int l_seq, id;                /* check if l_seq can be unsigned? */
-   char *name, *comment, *barcode, *qual, *sam; /* sam stored the end output of sam record */
+   char *name, *comment, *barcode, *umi, *qual, *sam; /* sam stored the end output of sam record */
    uint8_t *seq, *bisseq[2];
    uint8_t *seq0;              /* pointer to sequence beginning before clipping */
    int l_seq0;                 /* the original l_seq before clipping */

lib/aln/bwamem.h

@@ -120,7 +120,7 @@ typedef struct {
    int clip5;                   /* extra clip from 5'-end */
    int clip3;                   /* extra clip from 3'-end */
    int min_base_qual;           /* minimum base quality */
-   uint8_t has_bc;              /* read comment has barcode in it */
+   uint8_t has_bc;              /* read comment has barcode and UMI in it */
 } mem_opt_t;
 
 typedef struct {

lib/aln/mem_alnreg_format.c

@@ -401,9 +401,13 @@ void mem_alnreg_formatSAM(
     }
 
     if (s->barcode) {
-        kputsn("\tCR:Z:", 6, str);
+        kputsn("\tCB:Z:", 6, str);
         kputs(s->barcode, str);
     }
+    if (s->umi) {
+        kputsn("\tRX:Z:", 6, str);
+        kputs(s->umi, str);
+    }
 
     // MC/MQ: CIGAR string for mate/next segment (MC) and Mapping quality for mate/next segment (MQ)
     kputsn("\tMC:Z:", 6, str);