The pts and the corresponding duration is written in sidx
atoms, thus make sure these match up correctly.
---
 libavformat/movenc.c | 9 +++++++++
 libavformat/movenc.h | 1 +
 2 files changed, 10 insertions(+)

diff --git a/libavformat/movenc.c b/libavformat/movenc.c
index 3ba1cc8..5109fd7 100644
--- a/libavformat/movenc.c
+++ b/libavformat/movenc.c
@@ -3287,6 +3287,11 @@ int ff_mov_write_packet(AVFormatContext *s, AVPacket 
*pkt)
          * which might not exactly match our dts. Therefore adjust the dts
          * of this packet to be what the previous packets duration implies. */
         trk->cluster[trk->entry].dts = trk->start_dts + trk->track_duration;
+        /* We also may have written the pts and the corresponding duration
+         * in sidx tags; make sure the sidx pts and duration match up with
+         * the next fragment. This means the cts of the first sample must
+         * be the same in all fragments. */
+        pkt->pts = pkt->dts + trk->start_cts;
     }
     if (!trk->entry && trk->start_dts == AV_NOPTS_VALUE && !mov->use_editlist 
&&
         s->avoid_negative_ts == AVFMT_AVOID_NEG_TS_MAKE_ZERO) {
@@ -3315,6 +3320,9 @@ int ff_mov_write_packet(AVFormatContext *s, AVPacket *pkt)
         trk->flags |= MOV_TRACK_CTTS;
     trk->cluster[trk->entry].cts   = pkt->pts - pkt->dts;
     trk->cluster[trk->entry].flags = 0;
+    if (trk->start_cts == AV_NOPTS_VALUE)
+        trk->start_cts = pkt->pts - pkt->dts;
+
     if (enc->codec_id == AV_CODEC_ID_VC1) {
         mov_parse_vc1_frame(pkt, trk, mov->fragments);
     } else if (pkt->flags & AV_PKT_FLAG_KEY) {
@@ -3685,6 +3693,7 @@ static int mov_write_header(AVFormatContext *s)
          * this is updated. */
         track->hint_track = -1;
         track->start_dts  = AV_NOPTS_VALUE;
+        track->start_cts  = AV_NOPTS_VALUE;
         if (st->codec->codec_type == AVMEDIA_TYPE_VIDEO) {
             if (track->tag == MKTAG('m','x','3','p') || track->tag == 
MKTAG('m','x','3','n') ||
                 track->tag == MKTAG('m','x','4','p') || track->tag == 
MKTAG('m','x','4','n') ||
diff --git a/libavformat/movenc.h b/libavformat/movenc.h
index 4483b69..136bf13 100644
--- a/libavformat/movenc.h
+++ b/libavformat/movenc.h
@@ -104,6 +104,7 @@ typedef struct MOVTrack {
     uint32_t    tref_tag;
     int         tref_id; ///< trackID of the referenced track
     int64_t     start_dts;
+    int64_t     start_cts;
 
     int         hint_track;   ///< the track that hints this track, -1 if no 
hint track is set
     int         src_track;    ///< the track that this hint track describes
-- 
1.9.3 (Apple Git-50)

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