Add FASTQ_OPT_NCBI option for parsing of NCBI's SRA data.

hts.c

@@ -1035,6 +1035,10 @@ int hts_opt_add(hts_opt **opts, const char *c_arg) {
         strcmp(o->arg, "FASTQ_CASAVA") == 0)
         o->opt = FASTQ_OPT_CASAVA, o->val.i = 1;
 
+    else if (strcmp(o->arg, "fastq_name2") == 0 ||
+        strcmp(o->arg, "FASTQ_NAME2") == 0)
+        o->opt = FASTQ_OPT_NAME2, o->val.i = 1;
+
     else {
         hts_log_error("Unknown option '%s'", o->arg);
         free(o->arg);
@@ -1606,6 +1610,7 @@ int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...) {
 
     case FASTQ_OPT_CASAVA:
     case FASTQ_OPT_RNUM:
+    case FASTQ_OPT_NAME2:
         if (fp->format.format == fastq_format ||
             fp->format.format == fasta_format)
             return fastq_state_set(fp, opt);

htslib/hts.h

@@ -359,6 +359,11 @@ enum hts_fmt_option {
     // Two character string.
     // Barcode aux tag for CASAVA; defaults to "BC".
     FASTQ_OPT_BARCODE,
+
+    // Process SRA and ENA read names which pointlessly move the original
+    // name to the second field and insert a constructed <run>.<number>
+    // name in its place.
+    FASTQ_OPT_NAME2,
 };
 
 // Profile options for encoding; primarily used at present in CRAM

sam.c

@@ -3597,6 +3597,7 @@ typedef struct {
     char BC[3];         // aux tag ID for barcode
     khash_t(tag) *tags; // which aux tags to use (if empty, use all).
     char nprefix;
+    int sra_names;
 } fastq_state;
 
 // Initialise fastq state.
@@ -3640,6 +3641,10 @@ int fastq_state_set(samFile *fp, enum hts_fmt_option opt, ...) {
         x->casava = 1;
         break;
 
+    case FASTQ_OPT_NAME2:
+        x->sra_names = 1;
+        break;
+
     case FASTQ_OPT_AUX: {
         va_start(args, opt);
         x->aux = 1;
@@ -3710,11 +3715,27 @@ static int fastq_parse1(htsFile *fp, bam1_t *b) {
     }
 
     // Name
+
     if (*x->name.s != x->nprefix)
         return -2;
 
-    i = 0; l = x->name.l;
-    char *s = x->name.s;
+    // Reverse the SRA strangeness of putting the run_name.number before
+    // the read name.
+    i = 0;
+    char *name = x->name.s+1;
+    if (x->sra_names) {
+        char *cp = strpbrk(x->name.s, " \t");
+        if (cp) {
+            while (*cp == ' ' || *cp == '\t')
+                cp++;
+            *--cp = '@';
+            i = cp - x->name.s;
+            name = cp+1;
+        }
+    }
+
+    l = x->name.l;
+    char *s = x->name.s + i;
     while (i < l && !isspace_c(s[i]))
         i++;
     if (i < l) {
@@ -3774,7 +3795,7 @@ static int fastq_parse1(htsFile *fp, bam1_t *b) {
 
     // Convert to BAM
     ret = bam_set1(b,
-                   x->name.l-1, x->name.s+1,
+                   x->name.s + x->name.l - name, name,
                    flag,
                    -1, -1, 0, // ref '*', pos, mapq,
                    0, NULL,     // no cigar,

test/fastq/fastq.tst

@@ -77,6 +77,10 @@ P r2.sam $tview -i fastq_aux r2.fq
 P r1-q.sam $tview -i fastq_aux r1.fa
 P r2-q.sam $tview -i fastq_aux r2.fa
 
+# Simple tests for the FASTQ_NAME2 option.
+P name2.sam $tview -i fastq_name2 name2.fq
+P name2-q.sam $tview -i fastq_name2 name2.fa
+
 # --------------------
 # Writing
 

test/fastq/name2-q.sam

@@ -0,0 +1,4 @@
+name_001	4	*	0	0	*	*	0	0	CCGTTAGAGCATTTGTTGAAAATGCTTTCCTTGCTCCATGTGATGACTCTGGTGCCCTTGTCAAAAGCCAGCTGGGCCTATTCGTGTGGGTCTGTTTCTG	*
+name_002	4	*	0	0	*	*	0	0	TTGTTAAAATGACCATACCCAAAGTGATCTACAGACTCAATACAATTTCTATTGAAATACCAATCACACTCTTCACAGAACTAGAAAAACAGTTCTAAAA	*
+name_003	4	*	0	0	*	*	0	0	ACGCGGCAATCCAATGTGTGAGTTGAGAAGCGGTGAGGAGGGAATCCTAATTTTATGAGCAGGTCAGGACCGTGGGAGATACCTGACACCTGAGATGGTA	*
+name_004	4	*	0	0	*	*	0	0	GACATGCCATAACATTCATGTTTTATGTGTACAAGTCAATGAATTTTAGTATATTTACAGAGTTGTATGACTGTCTCCACAATCTAATTTTAGGTTTCCA	*

test/fastq/name2.fa

@@ -0,0 +1,8 @@
+>ignore_001 name_001
+CCGTTAGAGCATTTGTTGAAAATGCTTTCCTTGCTCCATGTGATGACTCTGGTGCCCTTGTCAAAAGCCAGCTGGGCCTATTCGTGTGGGTCTGTTTCTG
+>ignore_002	name_002
+TTGTTAAAATGACCATACCCAAAGTGATCTACAGACTCAATACAATTTCTATTGAAATACCAATCACACTCTTCACAGAACTAGAAAAACAGTTCTAAAA
+>ignore_003	     name_003
+ACGCGGCAATCCAATGTGTGAGTTGAGAAGCGGTGAGGAGGGAATCCTAATTTTATGAGCAGGTCAGGACCGTGGGAGATACCTGACACCTGAGATGGTA
+>name_004
+GACATGCCATAACATTCATGTTTTATGTGTACAAGTCAATGAATTTTAGTATATTTACAGAGTTGTATGACTGTCTCCACAATCTAATTTTAGGTTTCCA

test/fastq/name2.fq

@@ -0,0 +1,16 @@
+@ignore_001 name_001
+CCGTTAGAGCATTTGTTGAAAATGCTTTCCTTGCTCCATGTGATGACTCTGGTGCCCTTGTCAAAAGCCAGCTGGGCCTATTCGTGTGGGTCTGTTTCTG
++
+CABCFGDEEFFEFHGHGGFFGDIGIJFIFHHGHEIFGHBCGHDIFBE9GIAICGGICFIBFGGHGDGGGHE?GIGDFGGHEGIEJG>;FG<GGHACEFGH
+@ignore_002	name_002
+TTGTTAAAATGACCATACCCAAAGTGATCTACAGACTCAATACAATTTCTATTGAAATACCAATCACACTCTTCACAGAACTAGAAAAACAGTTCTAAAA
++
+CABEFGFFGFHGGGGJGGFFGKIHHJFIEHHHGIEGGEHJGHDHFGHIGICIJEFIFGIF8GGHKFHGGFEI6GGGFIGHGGIE>EFCFHGGGHEJEAJE
+@ignore_003	     name_003
+ACGCGGCAATCCAATGTGTGAGTTGAGAAGCGGTGAGGAGGGAATCCTAATTTTATGAGCAGGTCAGGACCGTGGGAGATACCTGACACCTGAGATGGTA
++
+BACCFGBFGFHGGJGHGGFEGHIGIJHFEH:HHEHGHHBGGH9IAGHGFHIFJFFAFGIFDIGHKEIG<C>F,CGD66?7EFI5EEG>EGGGGD5=HH6E
+@name_004
+GACATGCCATAACATTCATGTTTTATGTGTACAAGTCAATGAATTTTAGTATATTTACAGAGTTGTATGACTGTCTCCACAATCTAATTTTAGGTTTCCA
++
+CABFFGFFJFHEGEGJGGDG?FIGHHHBGHHHGIIGHGHGGHDGHFHIDFCIKEGIFHGGII9HFFGGGEEIGGEEHGGEEGDEHFH>FGGGGHAFAHGE

test/fastq/name2.sam

@@ -0,0 +1,4 @@
+name_001	4	*	0	0	*	*	0	0	CCGTTAGAGCATTTGTTGAAAATGCTTTCCTTGCTCCATGTGATGACTCTGGTGCCCTTGTCAAAAGCCAGCTGGGCCTATTCGTGTGGGTCTGTTTCTG	CABCFGDEEFFEFHGHGGFFGDIGIJFIFHHGHEIFGHBCGHDIFBE9GIAICGGICFIBFGGHGDGGGHE?GIGDFGGHEGIEJG>;FG<GGHACEFGH
+name_002	4	*	0	0	*	*	0	0	TTGTTAAAATGACCATACCCAAAGTGATCTACAGACTCAATACAATTTCTATTGAAATACCAATCACACTCTTCACAGAACTAGAAAAACAGTTCTAAAA	CABEFGFFGFHGGGGJGGFFGKIHHJFIEHHHGIEGGEHJGHDHFGHIGICIJEFIFGIF8GGHKFHGGFEI6GGGFIGHGGIE>EFCFHGGGHEJEAJE
+name_003	4	*	0	0	*	*	0	0	ACGCGGCAATCCAATGTGTGAGTTGAGAAGCGGTGAGGAGGGAATCCTAATTTTATGAGCAGGTCAGGACCGTGGGAGATACCTGACACCTGAGATGGTA	BACCFGBFGFHGGJGHGGFEGHIGIJHFEH:HHEHGHHBGGH9IAGHGFHIFJFFAFGIFDIGHKEIG<C>F,CGD66?7EFI5EEG>EGGGGD5=HH6E
+name_004	4	*	0	0	*	*	0	0	GACATGCCATAACATTCATGTTTTATGTGTACAAGTCAATGAATTTTAGTATATTTACAGAGTTGTATGACTGTCTCCACAATCTAATTTTAGGTTTCCA	CABFFGFFJFHEGEGJGGDG?FIGHHHBGHHHGIIGHGHGGHDGHFHIDFCIKEGIFHGGII9HFFGGGEEIGGEEHGGEEGDEHFH>FGGGGHAFAHGE