diff --git a/CMakeLists.txt b/CMakeLists.txt
index e97263a6..f8983067 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ add_compile_definitions("MAX_KMER_SIZE=${MAX_KMER_SIZE}")
 
 
 option(USE_HDF5 "Compile with HDF5 support" OFF) #OFF by default
-option(USE_BAM "Compile with HTSLIB support" OFF) # OFF by default
+option(USE_BAM "Compile with HTSLIB support" ON) # ON by défaut
 
 if(USE_HDF5)
     add_compile_definitions("USE_HDF5=ON")
diff --git a/src/ProcessReads.cpp b/src/ProcessReads.cpp
index 1d1e4fff..d7ad7f01 100755
--- a/src/ProcessReads.cpp
+++ b/src/ProcessReads.cpp
@@ -649,24 +649,52 @@ void MasterProcessor::update(const std::vector<uint32_t>& c, const std::vector<R
 void MasterProcessor::processAln(const EMAlgorithm& em, bool useEM = true) {
   // open bamfile and fetch header
   std::string bamfn = opt.output + "/pseudoalignments.bam";
+  bool is_cram = false;
+  // Mutually exclusive BAM/CRAM flags
+  if (opt.force_bam && opt.force_cram) {
+    std::cerr << "Error: --bam and --cram cannot be used together." << std::endl;
+    exit(1);
+  }
+  if (opt.force_cram) {
+    if (opt.reference_fasta.empty()) {
+      std::cerr << "[kallisto] Warning: --cram specified but --cram-reference missing. Falling back to BAM output." << std::endl;
+      bamfn = opt.output + "/pseudoalignments.bam";
+      is_cram = false;
+    } else {
+      bamfn = opt.output + "/pseudoalignments.cram";
+      is_cram = true;
+    }
+  } else if (opt.force_bam) {
+    bamfn = opt.output + "/pseudoalignments.bam";
+    is_cram = false;
+  } else if (opt.reference_fasta.size() > 0) {
+    bamfn = opt.output + "/pseudoalignments.cram";
+    is_cram = true;
+  } else if (bamfn.size() >= 5 && bamfn.substr(bamfn.size()-5) == ".cram") {
+    is_cram = true;
+  }
+
   if (opt.pseudobam) {
     if (opt.genomebam) {
       bamh = createPseudoBamHeaderGenome(model);
-
       bamfps = new htsFile*[numSortFiles];
       for (int i = 0; i < numSortFiles; i++) {
-        bamfps[i] = sam_open((opt.output + "/tmp." + std::to_string(i) + ".bam").c_str(), "wb1");
+        std::string tmpFile = opt.output + "/tmp." + std::to_string(i) + (is_cram ? ".cram" : ".bam");
+        bamfps[i] = sam_open(tmpFile.c_str(), is_cram ? "wc" : "wb1");
         int r = sam_hdr_write(bamfps[i], bamh);
+        if (is_cram && opt.reference_fasta.size() > 0) {
+          hts_set_fai_filename(bamfps[i], opt.reference_fasta.c_str());
+        }
       }
-
     } else {
       bamh = createPseudoBamHeaderTrans(index);
-      bamfp = sam_open(bamfn.c_str(), "wb");
+      bamfp = sam_open(bamfn.c_str(), is_cram ? "wc" : "wb");
       int r = sam_hdr_write(bamfp, bamh);
+      if (is_cram && opt.reference_fasta.size() > 0) {
+        hts_set_fai_filename(bamfp, opt.reference_fasta.c_str());
+      }
     }
-
     if (opt.threads > 1 && !opt.genomebam) {
-      // makes no sens to use threads on unsorted bams
       hts_set_threads(bamfp, opt.threads);
     }
   }
diff --git a/src/common.h b/src/common.h
index 3709021f..37e24d7a 100755
--- a/src/common.h
+++ b/src/common.h
@@ -91,6 +91,9 @@ struct BUSOptions {
 };
 
 struct ProgramOptions {
+  bool force_bam = false; // --bam
+  bool force_cram = false; // --cram
+  std::string bam_or_cram; // "bam" or "cram" to force output format
   bool verbose;
   bool aa;
   bool distinguish;
@@ -159,6 +162,7 @@ struct ProgramOptions {
   std::string genemap;
   std::string priors;
   std::string tmp_dir;
+  std::string reference_fasta; // chemin vers la référence pour CRAM
 
 ProgramOptions() :
   verbose(false),
diff --git a/src/main.cpp b/src/main.cpp
index 3d1097fb..8b2c0fc1 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -415,7 +415,8 @@ void ParseOptionsTCCQuant(int argc, char **argv, ProgramOptions& opt) {
     {"gtf", required_argument, 0, 'G'},
     {"bootstrap-samples", required_argument, 0, 'b'},
     {"seed", required_argument, 0, 'd'},
-    {"priors", required_argument, 0, 'p'}, 
+  {"priors", required_argument, 0, 'p'}, 
+  {"cram-reference", required_argument, 0, 1001}, // nouvelle option pour CRAM
     {0,0,0,0}
   };
   int c;
@@ -427,7 +428,7 @@ void ParseOptionsTCCQuant(int argc, char **argv, ProgramOptions& opt) {
       break;
     }
 
-    switch (c) {
+  switch (c) {
     case 0:
       break;
     case 't': {
@@ -487,6 +488,10 @@ void ParseOptionsTCCQuant(int argc, char **argv, ProgramOptions& opt) {
       opt.priors = optarg;
       break;
     }
+    case 1001: {
+      opt.reference_fasta = optarg;
+      break;
+    }
     default: break;
     }
   }
@@ -2130,7 +2135,8 @@ void usageBus() {
        << "    --aa                      Align to index generated from a FASTA-file containing amino acid sequences" << endl
        << "    --inleaved                Specifies that input is an interleaved FASTQ file" << endl
        << "    --batch-barcodes          Records both batch and extracted barcode in BUS file" << endl
-       << "    --verbose                 Print out progress information every 1M proccessed reads" << endl;
+  << "    --verbose                 Print out progress information every 1M proccessed reads" << endl
+  << "    --cram-reference=FASTA    Output CRAM using the provided FASTA reference (must be the same as for the index, enables .cram output)" << endl;
 }
 
 void usageIndex() {