diff --git a/fftools/ffmpeg.c b/fftools/ffmpeg.c
index 0be2715687..0944f56b80 100644
--- a/fftools/ffmpeg.c
+++ b/fftools/ffmpeg.c
@@ -141,8 +141,6 @@ unsigned nb_output_dumped = 0;
 static BenchmarkTimeStamps current_time;
 AVIOContext *progress_avio = NULL;
 
-InputStream **input_streams = NULL;
-int        nb_input_streams = 0;
 InputFile   **input_files   = NULL;
 int        nb_input_files   = 0;
 
@@ -279,7 +277,7 @@ static void sub2video_heartbeat(InputStream *ist, int64_t pts)
        video frames could be accumulating in the filter graph while a filter
        (possibly overlay) is desperately waiting for a subtitle frame. */
     for (i = 0; i < infile->nb_streams; i++) {
-        InputStream *ist2 = input_streams[infile->ist_index + i];
+        InputStream *ist2 = infile->streams[i];
         if (!ist2->sub2video.frame)
             continue;
         /* subtitles seem to be usually muxed ahead of other streams;
@@ -502,28 +500,6 @@ static int decode_interrupt_cb(void *ctx)
 
 const AVIOInterruptCB int_cb = { decode_interrupt_cb, NULL };
 
-static void ist_free(InputStream **pist)
-{
-    InputStream *ist = *pist;
-
-    if (!ist)
-        return;
-
-    av_frame_free(&ist->decoded_frame);
-    av_packet_free(&ist->pkt);
-    av_dict_free(&ist->decoder_opts);
-    avsubtitle_free(&ist->prev_sub.subtitle);
-    av_frame_free(&ist->sub2video.frame);
-    av_freep(&ist->filters);
-    av_freep(&ist->hwaccel_device);
-    av_freep(&ist->dts_buffer);
-
-    avcodec_free_context(&ist->dec_ctx);
-    avcodec_parameters_free(&ist->par);
-
-    av_freep(pist);
-}
-
 static void ffmpeg_cleanup(int ret)
 {
     int i, j;
@@ -580,9 +556,6 @@ static void ffmpeg_cleanup(int ret)
     for (i = 0; i < nb_input_files; i++)
         ifile_close(&input_files[i]);
 
-    for (i = 0; i < nb_input_streams; i++)
-        ist_free(&input_streams[i]);
-
     if (vstats_file) {
         if (fclose(vstats_file))
             av_log(NULL, AV_LOG_ERROR,
@@ -592,7 +565,6 @@ static void ffmpeg_cleanup(int ret)
     av_freep(&vstats_filename);
     av_freep(&filter_nbthreads);
 
-    av_freep(&input_streams);
     av_freep(&input_files);
     av_freep(&output_files);
 
@@ -628,6 +600,22 @@ static OutputStream *ost_iter(OutputStream *prev)
     return NULL;
 }
 
+InputStream *ist_iter(InputStream *prev)
+{
+    int if_idx  = prev ? prev->file_index : 0;
+    int ist_idx = prev ? prev->st->index + 1  : 0;
+
+    for (; if_idx < nb_input_files; if_idx++) {
+        InputFile *f = input_files[if_idx];
+        if (ist_idx < f->nb_streams)
+            return f->streams[ist_idx];
+
+        ist_idx = 0;
+    }
+
+    return NULL;
+}
+
 void remove_avoptions(AVDictionary **a, AVDictionary *b)
 {
     const AVDictionaryEntry *t = NULL;
@@ -1410,7 +1398,7 @@ static void print_final_stats(int64_t total_size)
                i, f->ctx->url);
 
         for (j = 0; j < f->nb_streams; j++) {
-            InputStream *ist = input_streams[f->ist_index + j];
+            InputStream *ist = f->streams[j];
             enum AVMediaType type = ist->par->codec_type;
 
             total_size    += ist->data_size;
@@ -2541,10 +2529,9 @@ static enum AVPixelFormat get_format(AVCodecContext *s, const enum AVPixelFormat
     return *p;
 }
 
-static int init_input_stream(int ist_index, char *error, int error_len)
+static int init_input_stream(InputStream *ist, char *error, int error_len)
 {
     int ret;
-    InputStream *ist = input_streams[ist_index];
 
     if (ist->decoding_needed) {
         const AVCodec *codec = ist->dec;
@@ -3163,12 +3150,12 @@ static int transcode_init(void)
         InputFile *ifile = input_files[i];
         if (ifile->readrate || ifile->rate_emu)
             for (j = 0; j < ifile->nb_streams; j++)
-                input_streams[j + ifile->ist_index]->start = av_gettime_relative();
+                ifile->streams[j]->start = av_gettime_relative();
     }
 
     /* init input streams */
-    for (i = 0; i < nb_input_streams; i++)
-        if ((ret = init_input_stream(i, error, sizeof(error))) < 0)
+    for (ist = ist_iter(NULL); ist; ist = ist_iter(ist))
+        if ((ret = init_input_stream(ist, error, sizeof(error))) < 0)
             goto dump_format;
 
     /*
@@ -3199,7 +3186,7 @@ static int transcode_init(void)
             int discard  = AVDISCARD_ALL;
 
             for (k = 0; k < p->nb_stream_indexes; k++)
-                if (!input_streams[ifile->ist_index + p->stream_index[k]]->discard) {
+                if (!ifile->streams[p->stream_index[k]]->discard) {
                     discard = AVDISCARD_DEFAULT;
                     break;
                 }
@@ -3210,9 +3197,7 @@ static int transcode_init(void)
  dump_format:
     /* dump the stream mapping */
     av_log(NULL, AV_LOG_INFO, "Stream mapping:\n");
-    for (i = 0; i < nb_input_streams; i++) {
-        ist = input_streams[i];
-
+    for (ist = ist_iter(NULL); ist; ist = ist_iter(ist)) {
         for (j = 0; j < ist->nb_filters; j++) {
             if (!filtergraph_is_simple(ist->filters[j]->graph)) {
                 av_log(NULL, AV_LOG_INFO, "  Stream #%d:%d (%s) -> %s",
@@ -3416,7 +3401,7 @@ static int check_keyboard_interaction(int64_t cur_time)
     if (key == 'd' || key == 'D'){
         int debug=0;
         if(key == 'D') {
-            debug = input_streams[0]->dec_ctx->debug << 1;
+            debug = ist_iter(NULL)->dec_ctx->debug << 1;
             if(!debug) debug = 1;
             while (debug & FF_DEBUG_DCT_COEFF) //unsupported, would just crash
                 debug += debug;
@@ -3434,9 +3419,8 @@ static int check_keyboard_interaction(int64_t cur_time)
             if (k <= 0 || sscanf(buf, "%d", &debug)!=1)
                 fprintf(stderr,"error parsing debug value\n");
         }
-        for(i=0;i<nb_input_streams;i++) {
-            input_streams[i]->dec_ctx->debug = debug;
-        }
+        for (InputStream *ist = ist_iter(NULL); ist; ist = ist_iter(ist))
+            ist->dec_ctx->debug = debug;
         for (OutputStream *ost = ost_iter(NULL); ost; ost = ost_iter(ost)) {
             if (ost->enc_ctx)
                 ost->enc_ctx->debug = debug;
@@ -3480,7 +3464,7 @@ static void reset_eagain(void)
 static void decode_flush(InputFile *ifile)
 {
     for (int i = 0; i < ifile->nb_streams; i++) {
-        InputStream *ist = input_streams[ifile->ist_index + i];
+        InputStream *ist = ifile->streams[i];
         int ret;
 
         if (!ist->processing_needed)
@@ -3627,7 +3611,7 @@ static int process_input(int file_index)
         }
 
         for (i = 0; i < ifile->nb_streams; i++) {
-            ist = input_streams[ifile->ist_index + i];
+            ist = ifile->streams[i];
             if (ist->processing_needed) {
                 ret = process_input_packet(ist, NULL, 0);
                 if (ret>0)
@@ -3650,7 +3634,7 @@ static int process_input(int file_index)
 
     reset_eagain();
 
-    ist = input_streams[ifile->ist_index + pkt->stream_index];
+    ist = ifile->streams[pkt->stream_index];
 
     ist->data_size += pkt->size;
     ist->nb_packets++;
@@ -3682,8 +3666,8 @@ static int process_input(int file_index)
     ts_discontinuity_process(ifile, ist, pkt);
 
     if (debug_ts) {
-        av_log(NULL, AV_LOG_INFO, "demuxer+ffmpeg -> ist_index:%d type:%s pkt_pts:%s pkt_pts_time:%s pkt_dts:%s pkt_dts_time:%s duration:%s duration_time:%s off:%s off_time:%s\n",
-               ifile->ist_index + pkt->stream_index,
+        av_log(NULL, AV_LOG_INFO, "demuxer+ffmpeg -> ist_index:%d:%d type:%s pkt_pts:%s pkt_pts_time:%s pkt_dts:%s pkt_dts_time:%s duration:%s duration_time:%s off:%s off_time:%s\n",
+               ifile->index, pkt->stream_index,
                av_get_media_type_string(ist->par->codec_type),
                av_ts2str(pkt->pts), av_ts2timestr(pkt->pts, &ist->st->time_base),
                av_ts2str(pkt->dts), av_ts2timestr(pkt->dts, &ist->st->time_base),
@@ -3887,8 +3871,7 @@ static int transcode(void)
     }
 
     /* at the end of stream, we must flush the decoder buffers */
-    for (i = 0; i < nb_input_streams; i++) {
-        ist = input_streams[i];
+    for (ist = ist_iter(NULL); ist; ist = ist_iter(ist)) {
         if (!input_files[ist->file_index]->eof_reached) {
             process_input_packet(ist, NULL, 0);
         }
@@ -3924,8 +3907,7 @@ static int transcode(void)
     }
 
     /* close each decoder */
-    for (i = 0; i < nb_input_streams; i++) {
-        ist = input_streams[i];
+    for (ist = ist_iter(NULL); ist; ist = ist_iter(ist)) {
         if (ist->decoding_needed) {
             avcodec_close(ist->dec_ctx);
         }
diff --git a/fftools/ffmpeg.h b/fftools/ffmpeg.h
index b1e466406d..5fc3b2d3d4 100644
--- a/fftools/ffmpeg.h
+++ b/fftools/ffmpeg.h
@@ -437,7 +437,6 @@ typedef struct InputFile {
     AVFormatContext *ctx;
     int eof_reached;      /* true if eof reached */
     int eagain;           /* true if last read attempt returned EAGAIN */
-    int ist_index;        /* index of first stream in input_streams */
     int64_t input_ts_offset;
     int input_sync_ref;
     /**
@@ -452,8 +451,13 @@ typedef struct InputFile {
     int64_t last_ts;
     int64_t start_time;   /* user-specified start time in AV_TIME_BASE or AV_NOPTS_VALUE */
     int64_t recording_time;
-    int nb_streams;       /* number of stream that ffmpeg is aware of; may be different
-                             from ctx.nb_streams if new streams appear during av_read_frame() */
+
+    /* streams that ffmpeg is aware of;
+     * there may be extra streams in ctx that are not mapped to an InputStream
+     * if new streams appear dynamically during demuxing */
+    InputStream **streams;
+    int        nb_streams;
+
     int rate_emu;
     float readrate;
     int accurate_seek;
@@ -629,8 +633,6 @@ typedef struct OutputFile {
     int bitexact;
 } OutputFile;
 
-extern InputStream **input_streams;
-extern int        nb_input_streams;
 extern InputFile   **input_files;
 extern int        nb_input_files;
 
@@ -766,6 +768,10 @@ void ifile_close(InputFile **f);
  */
 int ifile_get_packet(InputFile *f, AVPacket **pkt);
 
+/* iterate over all input streams in all input files;
+ * pass NULL to start iteration */
+InputStream *ist_iter(InputStream *prev);
+
 #define SPECIFIER_OPT_FMT_str  "%s"
 #define SPECIFIER_OPT_FMT_i    "%i"
 #define SPECIFIER_OPT_FMT_i64  "%"PRId64
diff --git a/fftools/ffmpeg_demux.c b/fftools/ffmpeg_demux.c
index 76778d774d..33035cd4d5 100644
--- a/fftools/ffmpeg_demux.c
+++ b/fftools/ffmpeg_demux.c
@@ -140,13 +140,13 @@ static int seek_to_start(Demuxer *d)
                 return ret;
             got_durations++;
 
-            ist = input_streams[ifile->ist_index + dur.stream_idx];
+            ist = ifile->streams[dur.stream_idx];
             ifile_duration_update(d, ist, dur.duration);
         }
     } else {
         for (int i = 0; i < ifile->nb_streams; i++) {
             int64_t duration = 0;
-            ist   = input_streams[ifile->ist_index + i];
+            ist   = ifile->streams[i];
 
             if (ist->framerate.num) {
                 duration = av_rescale_q(1, av_inv_q(ist->framerate), ist->st->time_base);
@@ -169,14 +169,14 @@ static int seek_to_start(Demuxer *d)
 static void ts_fixup(Demuxer *d, AVPacket *pkt, int *repeat_pict)
 {
     InputFile *ifile = &d->f;
-    InputStream *ist = input_streams[ifile->ist_index + pkt->stream_index];
+    InputStream *ist = ifile->streams[pkt->stream_index];
     const int64_t start_time = ifile->start_time_effective;
     int64_t duration;
 
     if (debug_ts) {
-        av_log(NULL, AV_LOG_INFO, "demuxer -> ist_index:%d type:%s "
+        av_log(NULL, AV_LOG_INFO, "demuxer -> ist_index:%d:%d type:%s "
                "pkt_pts:%s pkt_pts_time:%s pkt_dts:%s pkt_dts_time:%s duration:%s duration_time:%s\n",
-               ifile->ist_index + pkt->stream_index,
+               ifile->index, pkt->stream_index,
                av_get_media_type_string(ist->st->codecpar->codec_type),
                av_ts2str(pkt->pts), av_ts2timestr(pkt->pts, &ist->st->time_base),
                av_ts2str(pkt->dts), av_ts2timestr(pkt->dts, &ist->st->time_base),
@@ -381,7 +381,7 @@ static int thread_start(Demuxer *d)
         int nb_audio_dec = 0;
 
         for (int i = 0; i < f->nb_streams; i++) {
-            InputStream *ist = input_streams[f->ist_index + i];
+            InputStream *ist = f->streams[i];
             nb_audio_dec += !!(ist->decoding_needed &&
                                ist->st->codecpar->codec_type == AVMEDIA_TYPE_AUDIO);
         }
@@ -428,7 +428,7 @@ int ifile_get_packet(InputFile *f, AVPacket **pkt)
                              );
         float scale = f->rate_emu ? 1.0 : f->readrate;
         for (i = 0; i < f->nb_streams; i++) {
-            InputStream *ist = input_streams[f->ist_index + i];
+            InputStream *ist = f->streams[i];
             int64_t stream_ts_offset, pts, now;
             if (!ist->nb_packets || (ist->decoding_needed && !ist->got_output)) continue;
             stream_ts_offset = FFMAX(ist->first_dts != AV_NOPTS_VALUE ? ist->first_dts : 0, file_start);
@@ -447,13 +447,35 @@ int ifile_get_packet(InputFile *f, AVPacket **pkt)
     if (msg.looping)
         return 1;
 
-    ist = input_streams[f->ist_index + msg.pkt->stream_index];
+    ist = f->streams[msg.pkt->stream_index];
     ist->last_pkt_repeat_pict = msg.repeat_pict;
 
     *pkt = msg.pkt;
     return 0;
 }
 
+static void ist_free(InputStream **pist)
+{
+    InputStream *ist = *pist;
+
+    if (!ist)
+        return;
+
+    av_frame_free(&ist->decoded_frame);
+    av_packet_free(&ist->pkt);
+    av_dict_free(&ist->decoder_opts);
+    avsubtitle_free(&ist->prev_sub.subtitle);
+    av_frame_free(&ist->sub2video.frame);
+    av_freep(&ist->filters);
+    av_freep(&ist->hwaccel_device);
+    av_freep(&ist->dts_buffer);
+
+    avcodec_free_context(&ist->dec_ctx);
+    avcodec_parameters_free(&ist->par);
+
+    av_freep(pist);
+}
+
 void ifile_close(InputFile **pf)
 {
     InputFile *f = *pf;
@@ -464,6 +486,10 @@ void ifile_close(InputFile **pf)
 
     thread_stop(d);
 
+    for (int i = 0; i < f->nb_streams; i++)
+        ist_free(&f->streams[i]);
+    av_freep(&f->streams);
+
     avformat_close_input(&f->ctx);
 
     av_freep(pf);
@@ -562,10 +588,11 @@ static void add_display_matrix_to_stream(const OptionsContext *o,
                            vflip_set ? vflip : 0);
 }
 
-/* Add all the streams from the given input file to the global
- * list of input streams. */
-static void add_input_streams(const OptionsContext *o, AVFormatContext *ic)
+/* Add all the streams from the given input file to the demuxer */
+static void add_input_streams(const OptionsContext *o, Demuxer *d)
 {
+    InputFile       *f  = &d->f;
+    AVFormatContext *ic = f->ctx;
     int i, ret;
 
     for (i = 0; i < ic->nb_streams; i++) {
@@ -582,9 +609,9 @@ static void add_input_streams(const OptionsContext *o, AVFormatContext *ic)
         const AVOption *discard_opt = av_opt_find(&cc, "skip_frame", NULL,
                                                   0, AV_OPT_SEARCH_FAKE_OBJ);
 
-        ist = ALLOC_ARRAY_ELEM(input_streams, nb_input_streams);
+        ist = ALLOC_ARRAY_ELEM(f->streams, f->nb_streams);
         ist->st = st;
-        ist->file_index = nb_input_files;
+        ist->file_index = f->index;
         ist->discard = 1;
         st->discard  = AVDISCARD_ALL;
         ist->nb_samples = 0;
@@ -1013,24 +1040,16 @@ int ifile_open(const OptionsContext *o, const char *filename)
         }
     }
 
-    /* update the current parameters so that they match the one of the input stream */
-    add_input_streams(o, ic);
-
-    /* dump the file content */
-    av_dump_format(ic, nb_input_files, filename, 0);
-
     d = allocate_array_elem(&input_files, sizeof(*d), &nb_input_files);
     f = &d->f;
 
     f->ctx        = ic;
     f->index      = nb_input_files - 1;
-    f->ist_index  = nb_input_streams - ic->nb_streams;
     f->start_time = start_time;
     f->recording_time = recording_time;
     f->input_sync_ref = o->input_sync_ref;
     f->input_ts_offset = o->input_ts_offset;
     f->ts_offset  = o->input_ts_offset - (copy_ts ? (start_at_zero && ic->start_time != AV_NOPTS_VALUE ? ic->start_time : 0) : timestamp);
-    f->nb_streams = ic->nb_streams;
     f->rate_emu   = o->rate_emu;
     f->accurate_seek = o->accurate_seek;
     d->loop = o->loop;
@@ -1049,11 +1068,17 @@ int ifile_open(const OptionsContext *o, const char *filename)
 
     d->thread_queue_size = o->thread_queue_size;
 
+    /* update the current parameters so that they match the one of the input stream */
+    add_input_streams(o, d);
+
+    /* dump the file content */
+    av_dump_format(ic, f->index, filename, 0);
+
     /* check if all codec options have been used */
     unused_opts = strip_specifiers(o->g->codec_opts);
-    for (i = f->ist_index; i < nb_input_streams; i++) {
+    for (i = 0; i < f->nb_streams; i++) {
         e = NULL;
-        while ((e = av_dict_get(input_streams[i]->decoder_opts, "", e,
+        while ((e = av_dict_get(f->streams[i]->decoder_opts, "", e,
                                 AV_DICT_IGNORE_SUFFIX)))
             av_dict_set(&unused_opts, e->key, NULL, 0);
     }
diff --git a/fftools/ffmpeg_filter.c b/fftools/ffmpeg_filter.c
index 718826a485..5d50092b72 100644
--- a/fftools/ffmpeg_filter.c
+++ b/fftools/ffmpeg_filter.c
@@ -271,7 +271,7 @@ static void init_input_filter(FilterGraph *fg, AVFilterInOut *in)
                    "matches no streams.\n", p, fg->graph_desc);
             exit_program(1);
         }
-        ist = input_streams[input_files[file_idx]->ist_index + st->index];
+        ist = input_files[file_idx]->streams[st->index];
         if (ist->user_set_discard == AVDISCARD_ALL) {
             av_log(NULL, AV_LOG_FATAL, "Stream specifier '%s' in filtergraph description %s "
                    "matches a disabled input stream.\n", p, fg->graph_desc);
@@ -279,14 +279,13 @@ static void init_input_filter(FilterGraph *fg, AVFilterInOut *in)
         }
     } else {
         /* find the first unused stream of corresponding type */
-        for (i = 0; i < nb_input_streams; i++) {
-            ist = input_streams[i];
+        for (ist = ist_iter(NULL); ist; ist = ist_iter(ist)) {
             if (ist->user_set_discard == AVDISCARD_ALL)
                 continue;
             if (ist->dec_ctx->codec_type == type && ist->discard)
                 break;
         }
-        if (i == nb_input_streams) {
+        if (!ist) {
             av_log(NULL, AV_LOG_FATAL, "Cannot find a matching stream for "
                    "unlabeled input pad %d on filter %s\n", in->pad_idx,
                    in->filter_ctx->name);
diff --git a/fftools/ffmpeg_mux_init.c b/fftools/ffmpeg_mux_init.c
index 6db70cc852..b6782b49aa 100644
--- a/fftools/ffmpeg_mux_init.c
+++ b/fftools/ffmpeg_mux_init.c
@@ -171,7 +171,7 @@ static int get_preset_file_2(const char *preset_name, const char *codec_name, AV
 }
 
 static OutputStream *new_output_stream(Muxer *mux, const OptionsContext *o,
-                                       enum AVMediaType type, int source_index)
+                                       enum AVMediaType type, InputStream *ist)
 {
     AVFormatContext *oc = mux->fc;
     MuxStream     *ms;
@@ -354,8 +354,8 @@ static OutputStream *new_output_stream(Muxer *mux, const OptionsContext *o,
     if (ost->enc_ctx && av_get_exact_bits_per_sample(ost->enc_ctx->codec_id) == 24)
         av_dict_set(&ost->swr_opts, "output_sample_bits", "24", 0);
 
-    if (source_index >= 0) {
-        ost->ist = input_streams[source_index];
+    if (ist) {
+        ost->ist = ist;
         ost->ist->discard = 0;
         ost->ist->st->discard = ost->ist->user_set_discard;
     }
@@ -419,14 +419,14 @@ static void parse_matrix_coeffs(uint16_t *dest, const char *str)
     }
 }
 
-static OutputStream *new_video_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_video_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
     AVFormatContext *oc = mux->fc;
     AVStream *st;
     OutputStream *ost;
     char *frame_rate = NULL, *max_frame_rate = NULL, *frame_aspect_ratio = NULL;
 
-    ost = new_output_stream(mux, o, AVMEDIA_TYPE_VIDEO, source_index);
+    ost = new_output_stream(mux, o, AVMEDIA_TYPE_VIDEO, ist);
     st  = ost->st;
 
     MATCH_PER_STREAM_OPT(frame_rates, str, frame_rate, oc, st);
@@ -657,13 +657,13 @@ static OutputStream *new_video_stream(Muxer *mux, const OptionsContext *o, int s
     return ost;
 }
 
-static OutputStream *new_audio_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_audio_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
     AVFormatContext *oc = mux->fc;
     AVStream *st;
     OutputStream *ost;
 
-    ost = new_output_stream(mux, o, AVMEDIA_TYPE_AUDIO, source_index);
+    ost = new_output_stream(mux, o, AVMEDIA_TYPE_AUDIO, ist);
     st  = ost->st;
 
 
@@ -755,11 +755,11 @@ static OutputStream *new_audio_stream(Muxer *mux, const OptionsContext *o, int s
     return ost;
 }
 
-static OutputStream *new_data_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_data_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
     OutputStream *ost;
 
-    ost = new_output_stream(mux, o, AVMEDIA_TYPE_DATA, source_index);
+    ost = new_output_stream(mux, o, AVMEDIA_TYPE_DATA, ist);
     if (ost->enc_ctx) {
         av_log(NULL, AV_LOG_FATAL, "Data stream encoding not supported yet (only streamcopy)\n");
         exit_program(1);
@@ -768,11 +768,11 @@ static OutputStream *new_data_stream(Muxer *mux, const OptionsContext *o, int so
     return ost;
 }
 
-static OutputStream *new_unknown_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_unknown_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
     OutputStream *ost;
 
-    ost = new_output_stream(mux, o, AVMEDIA_TYPE_UNKNOWN, source_index);
+    ost = new_output_stream(mux, o, AVMEDIA_TYPE_UNKNOWN, ist);
     if (ost->enc_ctx) {
         av_log(NULL, AV_LOG_FATAL, "Unknown stream encoding not supported yet (only streamcopy)\n");
         exit_program(1);
@@ -781,19 +781,19 @@ static OutputStream *new_unknown_stream(Muxer *mux, const OptionsContext *o, int
     return ost;
 }
 
-static OutputStream *new_attachment_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_attachment_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
-    OutputStream *ost = new_output_stream(mux, o, AVMEDIA_TYPE_ATTACHMENT, source_index);
+    OutputStream *ost = new_output_stream(mux, o, AVMEDIA_TYPE_ATTACHMENT, ist);
     ost->finished    = 1;
     return ost;
 }
 
-static OutputStream *new_subtitle_stream(Muxer *mux, const OptionsContext *o, int source_index)
+static OutputStream *new_subtitle_stream(Muxer *mux, const OptionsContext *o, InputStream *ist)
 {
     AVStream *st;
     OutputStream *ost;
 
-    ost = new_output_stream(mux, o, AVMEDIA_TYPE_SUBTITLE, source_index);
+    ost = new_output_stream(mux, o, AVMEDIA_TYPE_SUBTITLE, ist);
     st  = ost->st;
 
     if (ost->enc_ctx) {
@@ -816,8 +816,8 @@ static void init_output_filter(OutputFilter *ofilter, const OptionsContext *o,
     OutputStream *ost;
 
     switch (ofilter->type) {
-    case AVMEDIA_TYPE_VIDEO: ost = new_video_stream(mux, o, -1); break;
-    case AVMEDIA_TYPE_AUDIO: ost = new_audio_stream(mux, o, -1); break;
+    case AVMEDIA_TYPE_VIDEO: ost = new_video_stream(mux, o, NULL); break;
+    case AVMEDIA_TYPE_AUDIO: ost = new_audio_stream(mux, o, NULL); break;
     default:
         av_log(NULL, AV_LOG_FATAL, "Only video and audio filters are supported "
                "currently.\n");
@@ -854,8 +854,8 @@ static void init_output_filter(OutputFilter *ofilter, const OptionsContext *o,
 static void map_auto_video(Muxer *mux, const OptionsContext *o)
 {
     AVFormatContext *oc = mux->fc;
-    InputStream *ist;
-    int best_score = 0, idx = -1;
+    InputStream *best_ist = NULL;
+    int best_score = 0;
     int qcr;
 
     /* video: highest resolution */
@@ -865,10 +865,11 @@ static void map_auto_video(Muxer *mux, const OptionsContext *o)
     qcr = avformat_query_codec(oc->oformat, oc->oformat->video_codec, 0);
     for (int j = 0; j < nb_input_files; j++) {
         InputFile *ifile = input_files[j];
-        int file_best_score = 0, file_best_idx = -1;
+        InputStream *file_best_ist = NULL;
+        int file_best_score = 0;
         for (int i = 0; i < ifile->nb_streams; i++) {
+            InputStream *ist = ifile->streams[i];
             int score;
-            ist = input_streams[ifile->ist_index + i];
 
             if (ist->user_set_discard == AVDISCARD_ALL ||
                 ist->st->codecpar->codec_type != AVMEDIA_TYPE_VIDEO)
@@ -884,27 +885,28 @@ static void map_auto_video(Muxer *mux, const OptionsContext *o)
                 if((qcr==MKTAG('A', 'P', 'I', 'C')) && !(ist->st->disposition & AV_DISPOSITION_ATTACHED_PIC))
                     continue;
                 file_best_score = score;
-                file_best_idx = ifile->ist_index + i;
+                file_best_ist   = ist;
             }
         }
-        if (file_best_idx >= 0) {
-            if((qcr == MKTAG('A', 'P', 'I', 'C')) || !(ist->st->disposition & AV_DISPOSITION_ATTACHED_PIC))
-                file_best_score -= 5000000*!!(input_streams[file_best_idx]->st->disposition & AV_DISPOSITION_DEFAULT);
+        if (file_best_ist) {
+            if((qcr == MKTAG('A', 'P', 'I', 'C')) ||
+               !(file_best_ist->st->disposition & AV_DISPOSITION_ATTACHED_PIC))
+                file_best_score -= 5000000*!!(file_best_ist->st->disposition & AV_DISPOSITION_DEFAULT);
             if (file_best_score > best_score) {
                 best_score = file_best_score;
-                idx = file_best_idx;
+                best_ist = file_best_ist;
             }
        }
     }
-    if (idx >= 0)
-        new_video_stream(mux, o, idx);
+    if (best_ist)
+        new_video_stream(mux, o, best_ist);
 }
 
 static void map_auto_audio(Muxer *mux, const OptionsContext *o)
 {
     AVFormatContext *oc = mux->fc;
-    InputStream *ist;
-    int best_score = 0, idx = -1;
+    InputStream *best_ist = NULL;
+    int best_score = 0;
 
         /* audio: most channels */
     if (av_guess_codec(oc->oformat, NULL, oc->url, NULL, AVMEDIA_TYPE_AUDIO) == AV_CODEC_ID_NONE)
@@ -912,10 +914,11 @@ static void map_auto_audio(Muxer *mux, const OptionsContext *o)
 
     for (int j = 0; j < nb_input_files; j++) {
         InputFile *ifile = input_files[j];
-        int file_best_score = 0, file_best_idx = -1;
+        InputStream *file_best_ist = NULL;
+        int file_best_score = 0;
         for (int i = 0; i < ifile->nb_streams; i++) {
+            InputStream *ist = ifile->streams[i];
             int score;
-            ist = input_streams[ifile->ist_index + i];
 
             if (ist->user_set_discard == AVDISCARD_ALL ||
                 ist->st->codecpar->codec_type != AVMEDIA_TYPE_AUDIO)
@@ -926,19 +929,19 @@ static void map_auto_audio(Muxer *mux, const OptionsContext *o)
                     + 5000000*!!(ist->st->disposition & AV_DISPOSITION_DEFAULT);
             if (score > file_best_score) {
                 file_best_score = score;
-                file_best_idx = ifile->ist_index + i;
+                file_best_ist   = ist;
             }
         }
-        if (file_best_idx >= 0) {
-            file_best_score -= 5000000*!!(input_streams[file_best_idx]->st->disposition & AV_DISPOSITION_DEFAULT);
+        if (file_best_ist) {
+            file_best_score -= 5000000*!!(file_best_ist->st->disposition & AV_DISPOSITION_DEFAULT);
             if (file_best_score > best_score) {
                 best_score = file_best_score;
-                idx = file_best_idx;
+                best_ist   = file_best_ist;
             }
        }
     }
-    if (idx >= 0)
-        new_audio_stream(mux, o, idx);
+    if (best_ist)
+        new_audio_stream(mux, o, best_ist);
 }
 
 static void map_auto_subtitle(Muxer *mux, const OptionsContext *o)
@@ -951,15 +954,15 @@ static void map_auto_subtitle(Muxer *mux, const OptionsContext *o)
     if (!avcodec_find_encoder(oc->oformat->subtitle_codec) && !subtitle_codec_name)
         return;
 
-    for (int i = 0; i < nb_input_streams; i++)
-        if (input_streams[i]->st->codecpar->codec_type == AVMEDIA_TYPE_SUBTITLE) {
+    for (InputStream *ist = ist_iter(NULL); ist; ist = ist_iter(ist))
+        if (ist->st->codecpar->codec_type == AVMEDIA_TYPE_SUBTITLE) {
             AVCodecDescriptor const *input_descriptor =
-                avcodec_descriptor_get(input_streams[i]->st->codecpar->codec_id);
+                avcodec_descriptor_get(ist->st->codecpar->codec_id);
             AVCodecDescriptor const *output_descriptor = NULL;
             AVCodec const *output_codec =
                 avcodec_find_encoder(oc->oformat->subtitle_codec);
             int input_props = 0, output_props = 0;
-            if (input_streams[i]->user_set_discard == AVDISCARD_ALL)
+            if (ist->user_set_discard == AVDISCARD_ALL)
                 continue;
             if (output_codec)
                 output_descriptor = avcodec_descriptor_get(output_codec->id);
@@ -973,7 +976,7 @@ static void map_auto_subtitle(Muxer *mux, const OptionsContext *o)
                 input_descriptor && output_descriptor &&
                 (!input_descriptor->props ||
                  !output_descriptor->props)) {
-                new_subtitle_stream(mux, o, i);
+                new_subtitle_stream(mux, o, ist);
                 break;
             }
         }
@@ -984,12 +987,16 @@ static void map_auto_data(Muxer *mux, const OptionsContext *o)
     AVFormatContext *oc = mux->fc;
     /* Data only if codec id match */
     enum AVCodecID codec_id = av_guess_codec(oc->oformat, NULL, oc->url, NULL, AVMEDIA_TYPE_DATA);
-    for (int i = 0; codec_id != AV_CODEC_ID_NONE && i < nb_input_streams; i++) {
-        if (input_streams[i]->user_set_discard == AVDISCARD_ALL)
+
+    if (codec_id == AV_CODEC_ID_NONE)
+        return;
+
+    for (InputStream *ist = ist_iter(NULL); ist; ist = ist_iter(ist)) {
+        if (ist->user_set_discard == AVDISCARD_ALL)
             continue;
-        if (input_streams[i]->st->codecpar->codec_type == AVMEDIA_TYPE_DATA
-            && input_streams[i]->st->codecpar->codec_id == codec_id )
-            new_data_stream(mux, o, i);
+        if (ist->st->codecpar->codec_type == AVMEDIA_TYPE_DATA &&
+            ist->st->codecpar->codec_id == codec_id )
+            new_data_stream(mux, o, ist);
     }
 }
 
@@ -1023,9 +1030,7 @@ loop_end:
         }
         init_output_filter(ofilter, o, mux);
     } else {
-        int src_idx = input_files[map->file_index]->ist_index + map->stream_index;
-
-        ist = input_streams[input_files[map->file_index]->ist_index + map->stream_index];
+        ist = input_files[map->file_index]->streams[map->stream_index];
         if (ist->user_set_discard == AVDISCARD_ALL) {
             av_log(NULL, AV_LOG_FATAL, "Stream #%d:%d is disabled and cannot be mapped.\n",
                    map->file_index, map->stream_index);
@@ -1041,14 +1046,14 @@ loop_end:
             return;
 
         switch (ist->st->codecpar->codec_type) {
-        case AVMEDIA_TYPE_VIDEO:      new_video_stream     (mux, o, src_idx); break;
-        case AVMEDIA_TYPE_AUDIO:      new_audio_stream     (mux, o, src_idx); break;
-        case AVMEDIA_TYPE_SUBTITLE:   new_subtitle_stream  (mux, o, src_idx); break;
-        case AVMEDIA_TYPE_DATA:       new_data_stream      (mux, o, src_idx); break;
-        case AVMEDIA_TYPE_ATTACHMENT: new_attachment_stream(mux, o, src_idx); break;
+        case AVMEDIA_TYPE_VIDEO:      new_video_stream     (mux, o, ist); break;
+        case AVMEDIA_TYPE_AUDIO:      new_audio_stream     (mux, o, ist); break;
+        case AVMEDIA_TYPE_SUBTITLE:   new_subtitle_stream  (mux, o, ist); break;
+        case AVMEDIA_TYPE_DATA:       new_data_stream      (mux, o, ist); break;
+        case AVMEDIA_TYPE_ATTACHMENT: new_attachment_stream(mux, o, ist); break;
         case AVMEDIA_TYPE_UNKNOWN:
             if (copy_unknown_streams) {
-                new_unknown_stream   (mux, o, src_idx);
+                new_unknown_stream   (mux, o, ist);
                 break;
             }
         default:
@@ -1096,7 +1101,7 @@ static void of_add_attachments(Muxer *mux, const OptionsContext *o)
         avio_read(pb, attachment, len);
         memset(attachment + len, 0, AV_INPUT_BUFFER_PADDING_SIZE);
 
-        ost = new_attachment_stream(mux, o, -1);
+        ost = new_attachment_stream(mux, o, NULL);
         ost->attachment_filename       = o->attachments[i];
         ost->st->codecpar->extradata      = attachment;
         ost->st->codecpar->extradata_size = len;
diff --git a/fftools/ffmpeg_opt.c b/fftools/ffmpeg_opt.c
index 61aa0be0ab..a9dcf0e088 100644
--- a/fftools/ffmpeg_opt.c
+++ b/fftools/ffmpeg_opt.c
@@ -417,7 +417,7 @@ static int opt_map(void *optctx, const char *opt, const char *arg)
                 if (check_stream_specifier(input_files[file_idx]->ctx, input_files[file_idx]->ctx->streams[i],
                             *p == ':' ? p + 1 : p) <= 0)
                     continue;
-                if (input_streams[input_files[file_idx]->ist_index + i]->user_set_discard == AVDISCARD_ALL) {
+                if (input_files[file_idx]->streams[i]->user_set_discard == AVDISCARD_ALL) {
                     disabled = 1;
                     continue;
                 }
@@ -523,7 +523,7 @@ static int opt_map_channel(void *optctx, const char *opt, const char *arg)
     if (allow_unused = strchr(mapchan, '?'))
         *allow_unused = 0;
     if (m->channel_idx < 0 || m->channel_idx >= st->codecpar->ch_layout.nb_channels ||
-        input_streams[input_files[m->file_idx]->ist_index + m->stream_idx]->user_set_discard == AVDISCARD_ALL) {
+        input_files[m->file_idx]->streams[m->stream_idx]->user_set_discard == AVDISCARD_ALL) {
         if (allow_unused) {
             av_log(NULL, AV_LOG_VERBOSE, "mapchan: invalid audio channel #%d.%d.%d\n",
                     m->file_idx, m->stream_idx, m->channel_idx);
