review update

header.c

@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2018-2020, 2023 Genome Research Ltd.
+Copyright (c) 2018-2020, 2023, 2025 Genome Research Ltd.
 Authors: James Bonfield <[email protected]>, Valeriu Ohan <[email protected]>
 
 Redistribution and use in source and binary forms, with or without
@@ -145,7 +145,7 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
         const char *name = NULL;
         const char *altnames = NULL;
         hts_pos_t len = -1;
-        int r, dup = 0;
+        int r, invLN = 0;
         khint_t k;
 
         while (tag) {
@@ -156,9 +156,8 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
                 assert(tag->len >= 3);
                 hts_pos_t tmp = len;
                 len = strtoll(tag->str+3, NULL, 10);
-                if (tmp != -1 && tmp != len) {
-                    //LN again with different value, discard
-                    dup = 1;
+                if (tmp != -1 && tmp != len) {  //duplicate and different LN
+                    invLN = 1;
                 }
             } else if (tag->str[0] == 'A' && tag->str[1] == 'N') {
                 assert(tag->len >= 3);
@@ -178,10 +177,10 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
             return -1; // LN should be present, according to spec.
         }
 
-        if (dup) {
-            hts_log_error("Header includes @SQ line \"%s\" with duplicate LN: tag", \
-                          name);
-            return -1;
+        if (invLN) {
+            hts_log_error("Header includes @SQ line \"%s\" with multiple LN:"
+            " tag with different values.", name);
+            return -1; // LN should not be duplicated or be same
         }
 
         // Seen already?

sam.c

@@ -1,6 +1,6 @@
 /*  sam.c -- SAM and BAM file I/O and manipulation.
 
-    Copyright (C) 2008-2010, 2012-2024 Genome Research Ltd.
+    Copyright (C) 2008-2010, 2012-2025 Genome Research Ltd.
     Copyright (C) 2010, 2012, 2013 Broad Institute.
 
     Author: Heng Li <[email protected]>
@@ -1911,12 +1911,6 @@ static sam_hdr_t *sam_hdr_sanitise(sam_hdr_t *h) {
         cp[h->l_text] = '\0';
     }
 
-     if (sam_hdr_fill_hrecs(h) < 0) {
-        //failed in parsing / validation
-        sam_hdr_destroy(h);
-        return NULL;
-    }
-
     return h;
 }
 
@@ -1972,13 +1966,13 @@ static sam_hdr_t *sam_hdr_create(htsFile* fp) {
                 } else {
                     if (strncmp(q, "LN:", 3) == 0) {
                         hts_pos_t tmp = strtoll(q + 3, (char**)&q, 10);
-                        if (ln != -1 && tmp != ln) {
-                            //duplicate LN tag with different value
-                            hts_log_error("111Header includes @SQ line \"%s\" with \
-duplicate LN: tag", sn);
+                        if (ln != -1 && ln != tmp) { //duplicate & different LN
+                            hts_log_error("Header includes @SQ line \"%s\" with"
+                                " multiple LN: tag with different values.", sn);
                             goto error;
+                        } else {
+                            ln = tmp;
                         }
-                        ln = tmp;
                     }
                 }